Bardet-Biedl susceptibility gene and uses thereof

ABSTRACT

The present invention relates to the identification of a gene, now designated negevin (ngvn), that is involved in the genetic disease Bardet Biedl Syndrome (BBS), which is characterized by such diverse symptoms as obesity, diabetes, hypertension, mental retardation, renal cancer and other abnormalities, retinopathy and hypogonadism. The human NGVN protein disclosed herein is 731 amino acids in length and is coded for by a gene spanning 17 exons. Homologs have been identified in mouse, rat, zebrafish. Methods of use for the gene, for example in diagnosis and therapy of BBS and in drug screening, also are described.

This application is a continuation of U.S. patent application Ser. No.11/370,242, filed on Mar. 7, 2006, which is a divisional of U.S. patentapplication Ser. No. 10/025,187, filed on Dec. 18, 2001, issued as U.S.Pat. No. 7,008,782 on Mar. 7, 2006, which claims priority to U.S.Provisional Patent Application Ser. No. 60/256,900 filed on Dec. 19,2000 and U.S. Provisional Patent Application Ser. No. 60/258,949 filedon Dec. 29, 2000. The entire text of the above-referenced applicationsare specifically incorporated herein by reference without disclaimer.

The government may own rights in the present invention pursuant to NIHgrant number R01-EY-11298.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates to the fields of genetics and molecularbiology. More particular the invention relates to the identification ofa gene on human chromosome 16 that is involved in Bardet-Biedl Syndrome(BBS), designated here as negevin (ngvn). Defects in this gene areassociated with a variety of clinical symptoms including diabetes, highblood pressure, renal cancer and other defects, retinal degeneration,congenital heart defects, limb deformity and obesity.

2. Description of Related Art

Bardet-Biedl Syndrome (BBS) is a rare, autosomal recessive disordercharacterized by mental retardation, obesity, pigmentary retinopathy,post-axial polydactyly and hypogonadism. A high frequency of renalabnormalities is also associated with this disorder. The mentalretardation is often mild. Obesity begins early in infancy, andcomplications of obesity including diabetes mellitus and hypertensionoccur later in life. The associated retinal degeneration is usuallysevere and most patients become blind prior to 20 years of age. A recentreport also provides evidence of an increased incidence of renal cellcarcinoma (kidney cancer) as well as kidney malformations in BBSsubjects.

The incidence of BBS varies between populations. A relatively highincidence of BBS is found in the mixed Arab populations of Kuwait andthe Bedouin tribes throughout the Middle East, most likely due to thehigh rate of consanguinity in these populations. A relatively highfrequency of BBS has also been reported in New Foundland.

BBS has been shown to display a remarkable degree of non-allelic geneticheterogeneity. The disorder was first shown to be geneticallyheterogenous based on mapping studies performed in large inbred Bedouinkindreds from Israel. The large number of traditional consanguineousmarriages within these groups make it possible to identify inbredkindreds with multiple affected individuals that are large enough forindependent linkage analysis.

The first BBS locus (now referred to as BBS2) was mapped to chromosome16 using a large inbred Bedouin kindred. Genetic heterogeneity wasdemonstrated when a second Bedouin BBS kindred did not map to thechromosome 16 locus. Subsequent studies in the second Bedouin kindredrevealed linkage to chromosome 3 (BBS3). A third Bedouin kindred showedlinkage to chromosome 15 (BBS4). To date, studies have demonstrated theexistence of six BBS loci, and a seventh BBS locus has been postulatedbased on the fact that a few small BBS pedigrees do not appear to map toany of the known loci. A locus on chromosome 11 was assigned thedesignation BBS1 based on the fact that it appears to be the most commoncause of BBS in some populations.

Recently, the first BBS gene (MKKS) was identified independently by twogroups that hypothesized that mutations in the gene causingMcKusick-Kaufman syndrome (MKS) could also cause BBS. MKS is anautosomal recessive disorder characterized by post-axial polydactyl), aswell as genital and cardiac anomalies. Mutations in the MKKS gene, aputative chaperonin gene, appear to account for approximately 10% of BBScases. The mechanism by which mutations in the MKKS gene cause BBS hasnot been determined.

Interest in the identification of genes causing BBS stem from thepleiotrophic nature of the disorder, and the fact that identification ofBBS genes may provide important insight into biochemical anddevelopmental pathways involved in common complex disorders includingobesity and diabetes mellitus.

SUMMARY OF THE INVENTION

Thus, in one aspect of the invention, there is provided an isolated andpurified nucleic acid encoding a human negevin (NGVN) polypeptide. Theamino acid sequence of SEQ ID NO:2 is exemplary, as are the nucleic acidsequences of SEQ ID NO:1 or SEQ ID NO:3. In addition, variants of thesequence included one or more of the changes selected from the groupconsisting of T₂₂₄→G, C₈₁₄→T, C₈₂₃→T, A₃₈₇→G, A₁₄₁₃→C, A₉₄₀del and1206insA. The nucleic acid may further comprise a promoter, for example,an inducible promoter, a constitutive promoter, or a tissue specificpromoter. It may also comprise a selectable marker, a poly-adenylationsignal and/or an origin of replication.

The nucleic acid may be part of a replicable vector, for example a viralvector such as a retroviral vector, an adenoviral vector, anadeno-associated viral vector, a herpes viral vector, a polyoma viralvector, a vaccinia viral vector or a lentiviral vector. The viral vectormay be located within a viral particle. The vector also may be anon-viral vector.

In another embodiment, there is provided an oligonucleotide of about 10to about 50 bases comprising at least 10 consecutive bases of SEQ IDNO:1 or SEQ ID NO:3, or the complement thereof. The oligonucleotide maybe 10, 15, 20, 25, 30, 35, 40, 45 or 50 bases in length, and may have10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 48, 49 or 50 consecutive bases of SEQ ID NO:1 or NO:3. Theoligonucleotide may encode or be complementary to a splice junction orregulatory region of SEQ ID NO:3. The oligonucleotide may encode or becomplementary to bases 224, 814, 823, 387, 1413, 940 or 1206 of SEQ IDNO:1. Also provided is human NGVN promoter isolatable from SEQ ID NO:3.

In still another embodiment, there is provided an isolated and purifiedhuman NGVN polypeptide, for example, comprising the sequence of SEQ IDNO:2. The polypeptide may also have one or more of the changes selectedfrom the group consisting of Val₇₅→Gly, Arg₂₇₂→Stop, Arg₂₇₅→Stop, andIle₁₂₃→Val. The polypeptide may comprises less than the entire NGVNsequence, for example, only residues 1-313 or 1-401 of SEQ ID NO:2. TheNGVN polypeptide also may be fused to a non-NGVN polypeptide.

In yet another embodiment, there is provided a method of expressing aNGVN polypeptide comprising transforming a host cell with an expressionconstruct encoding a NGVN polypeptide and culturing said host cell underconditions supporting expression of said NGVN polypeptide. The host cellmaybe a prokaryotic or a eukaryotic cell. The method may furthercomprise purifying said NGVN polypeptide. The expression construct maycomprise an inducible promoter, and the method may further compriseproviding to said host cell and inducer of said promoter.

In still yet another embodiment, there is provided a peptide of 8 to 50residues comprising at least 5 consecutive residues of SEQ ID NO:2. Thepeptide may be 10, 15, 20, 25, 30, 35, 40, 45 or 50 residues in length,and may comprise 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 or 50 consecutiveresidues of SEQ ID NO:2. The peptide may be bound to a carrier molecule,for example, by a linker. Also provided are a monoclonal antibody and apolyclonal antiserum that binds immunologically to a polypeptidecomprising the sequence of SEQ ID NO:2. The antibodies may be bound to asupport.

In still further embodiments, there are provided a method of diagnosingBardet-Biedl Syndrome (BBS), a method of diagnosing an individualgenetically predisposed to obesity, diabetes mellitus, retinopathy,hypertension, kidney cancer (renal carcinoma) and other renalabnormalities, congenital heart disease or limb defects comprisingidentifying a mutation in a NGVN polypeptide or nucleic acid. The methodmay comprise identifying a mutation in a NGVN polypeptide, for example,using immunologic analysis with a NGVN-binding monoclonal antibody orpolyclonal antiserum (e.g., ELISA, RIA, or Western blot). The method mayidentify a mutation selected from the group consisting of Val₇₅→Gly,Arg₂₇₂→Stop, Arg₂₇₅→Stop, and Ile₁₂₃→Val.

Alternatively, the method may comprise identifying a mutation in a NGVNnucleic acid, either mRNA, genomic DNA or cDNA. The method may compriseamplification of said nucleic acid, hybridization of said nucleic acidto a labeled nucleic acid probe, and/or sequencing of a NGVN nucleicacid. Again, the method may identify a mutation selected from the groupconsisting of T₂₂₄→G, C₈₁₄→T, C₈₂₃→T, A₃₈₇→G, A₁₄₁₃→C, A₉₄₀del and1206insA.

In still other embodiments, there are provided:

-   -   a method of screening for a modulator of NGVN expression        comprising (a) providing a cell expressing a NGVN        polypeptide; (b) contacting said cell with a candidate        modulator; (c) measuring NGVN expression; and (d) comparing said        NGVN expression in the presence of said candidate modulator with        the expression of NGVN in the absence of said candidate        modulator; wherein a difference in the expression of NGVN in the        presence of said candidate modulator, as compared with the        expression of NGVN in the absence of said candidate modulator,        identifies said candidate modulator as a modulator of NGVN        expression; and    -   a method of screening for a modulator of NGVN expression        comprising (a) providing a cell that comprises an expression        construct encoding an indicator polypeptide under the control of        a NGVN polypeptide; (b) contacting said cell with a candidate        modulator; (c) measuring expression of said indicator        polypeptide; and (d) comparing said expression of said indicator        polypeptide in the presence of said candidate modulator with the        expression of said indicator polypeptide in the absence of said        candidate modulator; wherein a difference in the expression of        said indicator polypeptide in the presence of said candidate        modulator, as compared with the expression of said indicator        polypeptide in the absence of said candidate modulator,        identifies said candidate modulator as a modulator of NGVN        expression; and    -   a method of producing a modulator of NGVN expression        comprising (a) providing a cell expressing a NGVN        polypeptide; (b) contacting said cell with a candidate        modulator; (c) measuring NGVN expression; (d) comparing said        NGVN expression in the presence of said candidate modulator with        the expression of NGVN in the absence of said candidate        modulator; wherein a difference in the expression of NGVN in the        presence of said candidate modulator, as compared with the        expression of NGVN in the absence of said candidate modulator,        identifies said candidate modulator as a modulator of NGVN        expression; and (e) producing the modulator; and    -   a modulator of NGVN expression produced according to the method        comprising (a) providing a cell expressing a NGVN        polypeptide; (b) contacting said cell with a candidate        modulator; (c) measuring NGVN expression; (d) comparing said        NGVN expression in the presence of said candidate modulator with        the expression of NGVN in the absence of said candidate        modulator; wherein a difference in the expression of NGVN in the        presence of said candidate modulator, as compared with the        expression of NGVN in the absence of said candidate modulator,        identifies said candidate modulator as a modulator of NGVN        expression; and (e) producing the modulator.

Other objects, features and advantages of the present invention willbecome apparent from the following detailed description. It should beunderstood, however, that the detailed description and the specificexamples, while indicating preferred embodiments of the invention, aregiven by way of illustration only, since various changes andmodifications within the spirit and scope of the invention will becomeapparent to those skilled in the art from this detailed description.

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

Bardet Biedl Syndrome (BBS) is a debilitating genetic disorder that isprevalent in Bedouin populations, probably due to the high consanguinityobserved therein. In order to identify the gene causing BBS2, theinventors used genetic fine mapping to reduce the size of the BBS2interval on chromosome 16 from the previously reported interval of 18cM. Fine mapping looking at shared haplotypes of affected individualswithin the extended Bedouin kindred only made it possible to narrow theinterval to approximately 6 cM. Therefore, it was decided to search forunaffected individuals within the extended kindred who had the completeaffected haplotype on one chromosome, but were recombinant for theaffected haplotype on the homologous chromosome. Two such individualswere identified, and the recombination events within these individualsgreatly reduced the candidate interval to approximately 3 cM. Theability to narrow the disease interval using data from the Bedouinkindred made it possible to construct a physical map across the diseaseinterval.

The identification of the BBS2 gene was aided by sample sequencing(approximately 1× coverage), as well as sequence data from the HumanGenome Project. Analysis of this sequence resulted in the identificationof a number of candidate genes within the narrowest interval. In orderto determine which of these genes was the BBS2 gene, the inventorsundertook to prioritize the genes for mutation screening based on anumber of parameters including sequence homology or a putativefunctional relationship to genes in other known BBS intervals, as wellas tissue pattern of expression. Although this approach yielded a numberof high priority candidate genes, none of these genes proved to bemutated in BBS patients. The recent identification of BBS causingmutations in the MKKS gene provided initial speculation that achaperonin gene might be found in this interval. A search of theavailable sequence in the interval failed to identify such a candidategene.

Due to the non-allelic genetic heterogeneity of BBS, the strategy formutation screening of candidate genes was to focus the search formutations by direct DNA sequencing of DNA from a proband from each oftwo inbred families shown to link to the chromosome 16 BBS interval. Oneof the families was the large Bedouin kindred that was used to initiallymap and refine the 16q21 interval. Sequencing of probands from inbredfamilies provided the advantage of looking for homozygous sequencevariations compared to control sequence. Homozygous changes are morereadily recognized compared to heterozygous mutations by directsequencing. Sequencing revealed homozygous mutations in the negevin(ngvn) gene in each of the two inbred families. Each mutation was shownto segregate completely with the disease phenotype in the respectivekindreds, and neither mutation was found in 96 control individuals.After the identification of mutations in NGVN in both of the linkedfamilies, the inventors screened an additional 18 probands for NGVNmutations. A total of 4 probands (22%) had mutations, a figure that isconsistent with the proportion of BBS2 cases reported in the literature.

The conclusion that NGVN is the BBS2 gene is supported by a number oflines of evidence. First, it maps to the narrowed disease interval andhas a broad pattern of tissue expression as would be predicted for apleiotrophic gene. Second, it is found to have homozygous mutations intwo inbred pedigrees, one of which is a frameshift. And third, it ismutated (both nonsense and frameshift) in a number of isolated BBSprobands and small families. Together, the evidence strongly supportsthe conclusion that NGVN is responsible for the BBS2 phenotype.

The inventors have previously hypothesized that the identification ofthe first BBS gene would lead to the rapid identification of other BBSgenes. In the case of MKKS, this has not yet proven to be the case, asNGVN has no significant sequence homology to MKKS and no currently knownfunctional relationship. Despite this fact, the inventors hypothesizethat a functional relationship does exist. It is possible that NGVNplays an unrecognized chaperonin role or is part of a chaperonincomplex. Another possibility is that NGVN is a substrate of MKKSchaperonin function.

The identification of NGVN has immediate implications for the isolatedBedouin community that was used in the initial mapping and that has ahigh incidence of the disease. Population-wide carrier testing could nowbe efficiently performed to accurately identify disease gene carriers.Such a program would have the potential of decreasing the burden of thisdisorder in this isolated community. Detection of carriers might beparticularly useful in this society since the vast majority of marriagesare arranged. In addition, the present invention also provides theopportunity for therapeutic intervention, as well as drug screening toidentify therapeutic agents. This and other embodiments are described ingreater detail below.

1. NGVN Protein

The protein sequence for human negevin is provided in SEQ ID NO:2. Inaddition to the entire NGVN molecule, the present invention also relatesto fragments of the polypeptides that may or may not retain various ofthe functions described below. Fragments, including the N-terminus ofthe molecule may be generated by genetic engineering of translation stopsites within the coding region (discussed below). Alternatively,treatment of the NGVN with proteolytic enzymes, known as proteases, canproduces a variety of N-terminal, C-terminal and internal fragments.Peptides range from 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, and 50residues, such as those made synthetically, up to 100, 150, 200, 250,300, 350, 400, 450, 500, 550, 600, 650, 700 and more residues, which areconveniently produced by recombinant means or by proteolytic digestionof full length NGVN. Examples of fragments may include contiguousresidues of SEQ ID NO:2 of 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 75, 80,85, 90, 95, 100, 200, 300, 400 or more amino acids in length. Thesefragments may be purified according to known methods, such asprecipitation (e.g., ammonium sulfate), HPLC, ion exchangechromatography, affinity chromatography (including immunoaffinitychromatography) or various size separations (sedimentation, gelelectrophoresis, gel filtration).

A. Variants of NGVN

Amino acid sequence variants of the NGVN polypeptide can besubstitutional, insertional or deletion variants. Deletion variants lackone or more residues of the native protein which are not essential forfunction or immunogenic activity, and are exemplified by the variantslacking a transmembrane sequence described above. Another common type ofdeletion variant is one lacking secretory signal sequences or signalsequences directing a protein to bind to a particular part of a cell.Insertional mutants typically involve the addition of material at anon-terminal point in the polypeptide. This may include the insertion ofan immunoreactive epitope or simply a single residue. Terminaladditions, called fusion proteins, are discussed below.

Substitutional variants typically contain the exchange of one amino acidfor another at one or more sites within the protein, and may be designedto modulate one or more properties of the polypeptide, such as stabilityagainst proteolytic cleavage, without the loss of other functions orproperties. Substitutions of this kind preferably are conservative, thatis, one amino acid is replaced with one of similar shape and charge.Conservative substitutions are well known in the art and include, forexample, the changes of alanine to serine; arginine to lysine;asparagine to glutamine or histidine; aspartate to glutamate; cysteineto serine; glutamine to asparagine; glutamate to aspartate; glycine toproline; histidine to asparagine or glutamine; isoleucine to leucine orvaline; leucine to valine or isoleucine; lysine to arginine; methionineto leucine or isoleucine; phenylalanine to tyrosine, leucine ormethionine; serine to threonine; threonine to serine; tryptophan totyrosine; tyrosine to tryptophan or phenylalanine; and valine toisoleucine or leucine.

The following is a discussion based upon changing of the amino acids ofa protein to create an equivalent, or even an improved,second-generation molecule. For example, certain amino acids may besubstituted for other amino acids in a protein structure withoutappreciable loss of interactive binding capacity with structures suchas, for example, antigen-binding regions of antibodies or binding siteson substrate molecules. Since it is the interactive capacity and natureof a protein that defines that protein's biological functional activity,certain amino acid substitutions can be made in a protein sequence, andits underlying DNA coding sequence, and nevertheless obtain a proteinwith like properties. It is thus contemplated by the inventors thatvarious changes may be made in the DNA sequences of genes withoutappreciable loss of their biological utility or activity, as discussedbelow. Table 1 shows the codons that encode particular amino acids.

In making such changes, the hydropathic index of amino acids may beconsidered. The importance of the hydropathic amino acid index inconferring interactive biologic function on a protein is generallyunderstood in the art (Kyte and Doolittle, 1982). It is accepted thatthe relative hydropathic character of the amino acid contributes to thesecondary structure of the resultant protein, which in turn defines theinteraction of the protein with other molecules, for example, enzymes,substrates, receptors, DNA, antibodies, antigens, and the like.

Each amino acid has been assigned a hydropathic index on the basis oftheir hydrophobicity and charge characteristics (Kyte and Doolittle,1982), these are: isoleucine (+4.5); valine (+4.2); leucine (+3.8);phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9);alanine (+1.8); glycine (−0.4); threonine (−0.7); serine (−0.8);tryptophan (−0.9); tyrosine (−1.3); proline (−1.6); histidine (−3.2);glutamate (−3.5); glutamine (−3.5); aspartate (−3.5); asparagine (−3.5);lysine (−3.9); and arginine (−4.5).

It is known in the art that certain amino acids may be substituted byother amino acids having a similar hydropathic index or score and stillresult in a protein with similar biological activity, i.e., still obtaina biological functionally equivalent protein. In making such changes,the substitution of amino acids whose hydropathic indices are within ±2is preferred, those which are within ±1 are particularly preferred, andthose within ±0.5 are even more particularly preferred.

It is also understood in the art that the substitution of like aminoacids can be made effectively on the basis of hydrophilicity. U.S. Pat.No. 4,554,101, incorporated herein by reference, states that thegreatest local average hydrophilicity of a protein, as governed by thehydrophilicity of its adjacent amino acids, correlates with a biologicalproperty of the protein. As detailed in U.S. Pat. No. 4,554,101, thefollowing hydrophilicity values have been assigned to amino acidresidues: arginine (+3.0); lysine (+3.0); aspartate (+3.0±1); glutamate(+3.0±1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine(0); threonine (−0.4); proline (−0.5±1); alanine (−0.5); histidine(−0.5); cysteine (−1.0); methionine (−1.3); valine (−1.5); leucine(−1.8); isoleucine (−1.8); tyrosine (−2.3); phenylalanine (−2.5);tryptophan (−3.4).

It is understood that an amino acid can be substituted for anotherhaving a similar hydrophilicity value and still obtain a biologicallyequivalent and immunologically equivalent protein. In such changes, thesubstitution of amino acids whose hydrophilicity values are within 12 ispreferred, those that are within ±1 are particularly preferred, andthose within ±0.5 are even more particularly preferred.

As outlined above, amino acid substitutions are generally based on therelative similarity of the amino acid side-chain substituents, forexample, their hydrophobicity, hydrophilicity, charge, size, and thelike. Exemplary substitutions that take various of the foregoingcharacteristics into consideration are well known to those of skill inthe art and include: arginine and lysine; glutamate and aspartate;serine and threonine; glutamine and asparagine; and valine, leucine andisoleucine.

Another embodiment for the preparation of polypeptides according to theinvention is the use of peptide mimetics. Mimetics arepeptide-containing molecules that mimic elements of protein secondarystructure (Johnson et al, 1993). The underlying rationale behind the useof peptide mimetics is that the peptide backbone of proteins existschiefly to orient amino acid side chains in such a way as to facilitatemolecular interactions, such as those of antibody and antigen. A peptidemimetic is expected to permit molecular interactions similar to thenatural molecule. These principles may be used, in conjunction with theprinciples outline above, to engineer second generation molecules havingmany of the natural properties of NGVN, but with altered and evenimproved characteristics.

B. Domain Switching

As described in the examples, the present inventors have identifiedmurine and rat NGVN, in addition to humans. An interesting series ofmutants can be created by substituting homologous regions of variousproteins. This is known, in certain contexts, as “domain switching.”

Domain switching involves the generation of chimeric molecules usingdifferent but, in this case, related polypeptides. By comparing variousNGVN proteins, one can make predictions as to the functionallysignificant regions of these molecules. It is possible, then, to switchrelated domains of these molecules in an effort to determine thecriticality of these regions to NGVN function. These molecules may haveadditional value in that these “chimeras” can be distinguished fromnatural molecules, while possibly providing the same function.

C. Fusion Proteins

A specialized kind of insertional variant is the fusion protein. Thismolecule generally has all or a substantial portion of the nativemolecule, linked at the N- or C-terminus, to all or a portion of asecond polypeptide. For example, fusions typically employ leadersequences from other species to permit the recombinant expression of aprotein in a heterologous host. Another useful fusion includes theaddition of a immunologically active domain, such as an antibodyepitope, to facilitate purification of the fusion protein. Inclusion ofa cleavage site at or near the fusion junction will facilitate removalof the extraneous polypeptide after purification. Other useful fusionsinclude linking of functional domains, such as active sites fromenzymes, glycosylation domains, cellular targeting signals ortransmembrane regions.

D. Purification of Proteins

It will be desirable to purify NGVN or variants thereof. Proteinpurification techniques are well known to those of skill in the art.These techniques involve, at one level, the crude fractionation of thecellular milieu to polypeptide and non-polypeptide fractions. Havingseparated the polypeptide from other proteins, the polypeptide ofinterest may be further purified using chromatographic andelectrophoretic techniques to achieve partial or complete purification(or purification to homogeneity). Analytical methods particularly suitedto the preparation of a pure peptide are ion-exchange chromatography,exclusion chromatography; polyacrylamide gel electrophoresis;isoelectric focusing. A particularly efficient method of purifyingpeptides is fast protein liquid chromatography or even HPLC.

Certain aspects of the present invention concern the purification, andin particular embodiments, the substantial purification, of an encodedprotein or peptide. The term “purified protein or peptide” as usedherein, is intended to refer to a composition, isolatable from othercomponents, wherein the protein or peptide is purified to any degreerelative to its naturally-obtainable state. A purified protein orpeptide therefore also refers to a protein or peptide, free from theenvironment in which it may naturally occur.

Generally, “purified” will refer to a protein or peptide compositionthat has been subjected to fractionation to remove various othercomponents, and which composition substantially retains its expressedbiological activity. Where the term “substantially purified” is used,this designation will refer to a composition in which the protein orpeptide forms the major component of the composition, such asconstituting about 50%, about 60%, about 70%, about 80%, about 90%,about 95% or more of the proteins in the composition.

Various methods for quantifying the degree of purification of theprotein or peptide will be known to those of skill in the art in lightof the present disclosure. These include, for example, determining thespecific activity of an active fraction, or assessing the amount ofpolypeptides within a fraction by SDS/PAGE analysis. A preferred methodfor assessing the purity of a fraction is to calculate the specificactivity of the fraction, to compare it to the specific activity of theinitial extract, and to thus calculate the degree of purity, hereinassessed by a “-fold purification number.” The actual units used torepresent the amount of activity will, of course, be dependent upon theparticular assay technique chosen to follow the purification and whetheror not the expressed protein or peptide exhibits a detectable activity.

Various techniques suitable for use in protein purification will be wellknown to those of skill in the art. These include, for example,precipitation with ammonium sulphate, PEG, antibodies and the like or byheat denaturation, followed by centrifugation; chromatography steps suchas ion exchange, gel filtration, reverse phase, hydroxylapatite andaffinity chromatography; isoelectric focusing; gel electrophoresis; andcombinations of such and other techniques. As is generally known in theart, it is believed that the order of conducting the variouspurification steps may be changed, or that certain steps may be omitted,and still result in a suitable method for the preparation of asubstantially purified protein or peptide.

There is no general requirement that the protein or peptide always beprovided in their most purified state. Indeed, it is contemplated thatless substantially purified products will have utility in certainembodiments. Partial purification may be accomplished by using fewerpurification steps in combination, or by utilizing different forms ofthe same general purification scheme. For example, it is appreciatedthat a cation-exchange column chromatography performed utilizing an HPLCapparatus will generally result in a greater “-fold” purification thanthe same technique utilizing a low pressure chromatography system.Methods exhibiting a lower degree of relative purification may haveadvantages in total recovery of protein product, or in maintaining theactivity of an expressed protein.

It is known that the migration of a polypeptide can vary, sometimessignificantly, with different conditions of SDS/PAGE (Capaldi et al.,1977). It will therefore be appreciated that under differingelectrophoresis conditions, the apparent molecular weights of purifiedor partially purified expression products may vary.

High Performance Liquid Chromatography (HPLC) is characterized by a veryrapid separation with extraordinary resolution of peaks. This isachieved by the use of very fine particles and high pressure to maintainan adequate flow rate. Separation can be accomplished in a matter ofminutes, or at most an hour. Moreover, only a very small volume of thesample is needed because the particles are so small and close-packedthat the void volume is a very small fraction of the bed volume. Also,the concentration of the sample need not be very great because the bandsare so narrow that there is very little dilution of the sample.

Gel chromatography, or molecular sieve chromatography, is a special typeof partition chromatography that is based on molecular size. The theorybehind gel chromatography is that the column, which is prepared withtiny particles of an inert substance that contain small pores, separateslarger molecules from smaller molecules as they pass through or aroundthe pores, depending on their size. As long as the material of which theparticles are made does not adsorb the molecules, the sole factordetermining rate of flow is the size. Hence, molecules are eluted fromthe column in decreasing size, so long as the shape is relativelyconstant. Gel chromatography is unsurpassed for separating molecules ofdifferent size because separation is independent of all other factorssuch as pH, ionic strength, temperature, etc. There also is virtually noadsorption, less zone spreading and the elution volume is related in asimple matter to molecular weight.

Affinity Chromatography is a chromatographic procedure that relies onthe specific affinity between a substance to be isolated and a moleculethat it can specifically bind to. This is a receptor-ligand typeinteraction. The column material is synthesized by covalently couplingone of the binding partners to an insoluble matrix. The column materialis then able to specifically adsorb the substance from the solution.Elution occurs by changing the conditions to those in which binding willnot occur (alter pH, ionic strength, temperature, etc.).

A particular type of affinity chromatography useful in the purificationof carbohydrate containing compounds is lectin affinity chromatography.Lectins are a class of substances that bind to a variety ofpolysaccharides and glycoproteins. Lectins are usually coupled toagarose by cyanogen bromide. Conconavalin A coupled to Sepharose was thefirst material of this sort to be used and has been widely used in theisolation of polysaccharides and glycoproteins other lectins that havebeen include lentil lectin, wheat germ agglutinin which has been usefulin the purification of N-acetyl glucosaminyl residues and Helix pomatialectin. Lectins themselves are purified using affinity chromatographywith carbohydrate ligands. Lactose has been used to purify lectins fromcastor bean and peanuts; maltose has been useful in extracting lectinsfrom lentils and jack bean; N-acetyl-D galactosamine is used forpurifying lectins from soybean; N-acetyl glucosaminyl binds to lectinsfrom wheat germ; D-galactosamine has been used in obtaining lectins fromclams and L-fucose will bind to lectins from lotus.

The matrix should be a substance that itself does not adsorb moleculesto any significant extent and that has a broad range of chemical,physical and thermal stability. The ligand should be coupled in such away as to not affect its binding properties. The ligand should alsoprovide relatively tight binding. And it should be possible to elute thesubstance without destroying the sample or the ligand. One of the mostcommon forms of affinity chromatography is immunoaffinitychromatography. The generation of antibodies that would be suitable foruse in accord with the present invention is discussed below.

E. Synthetic Peptides

The present invention also describes smaller NGVN-related peptides foruse in various embodiments of the present invention. Because of theirrelatively small size, the peptides of the invention can also besynthesized in solution or on a solid support in accordance withconventional techniques. Various automatic synthesizers are commerciallyavailable and can be used in accordance with known protocols. See, forexample, Stewart and Young, (1984); Tam et al., (1983); Merrifield,(1986); and Barany and Merrifield (1979), each incorporated herein byreference. Short peptide sequences, or libraries of overlappingpeptides, usually from about 6 up to about 35 to 50 amino acids, whichcorrespond to the selected regions described herein, can be readilysynthesized and then screened in screening assays designed to identifyreactive peptides. Alternatively, recombinant DNA technology may beemployed wherein a nucleotide sequence which encodes a peptide of theinvention is inserted into an expression vector, transformed ortransfected into an appropriate host cell and cultivated underconditions suitable for expression.

F. Antigen Compositions

The present invention also provides for the use of NGVN proteins orpeptides as antigens for the immunization of animals relating to theproduction of antibodies. It is envisioned that NGVN or portionsthereof, will be coupled, bonded, bound, conjugated or chemically-linkedto one or more agents via linkers, polylinkers or derivatized aminoacids. This may be performed such that a bispecific or multivalentcomposition or vaccine is produced. It is further envisioned that themethods used in the preparation of these compositions will be familiarto those of skill in the art and should be suitable for administrationto animals, i.e., pharmaceutically acceptable. Preferred agents are thecarriers are keyhole limpet hemocyannin (KLH) or bovine serum albumin(BSA).

G. Antibody Production

In certain embodiments, the present invention provides antibodies thatbind with high specificity to the NGVN polypeptides provided herein.Thus, antibodies that bind to the polypeptide of SEQ ID NO:2 areprovided. In addition to antibodies generated against the full lengthproteins, antibodies may also be generated in response to smallerconstructs comprising epitopic core regions, including wild-type andmutant epitopes.

As used herein, the term “antibody” is intended to refer broadly to anyimmunologic binding agent such as IgG, IgM, IgA, IgD and IgE. Generally,IgG and/or IgM are preferred because they are the most common antibodiesin the physiological situation and because they are most easily made ina laboratory setting.

Monoclonal antibodies (MAbs) are recognized to have certain advantages,e.g., reproducibility and large-scale production, and their use isgenerally preferred. The invention thus provides monoclonal antibodiesof the human, murine, monkey, rat, hamster, rabbit and even chickenorigin. Due to the ease of preparation and ready availability ofreagents, murine monoclonal antibodies will often be preferred.

However, “humanized” antibodies are also contemplated, as are chimericantibodies from mouse, rat, or other species, bearing human constantand/or variable region domains, bispecific antibodies, recombinant andengineered antibodies and fragments thereof. Methods for the developmentof antibodies that are “custom-tailored” to the patient's dental diseaseare likewise known and such custom-tailored antibodies are alsocontemplated.

The term “antibody” is used to refer to any antibody-like molecule thathas an antigen binding region, and includes antibody fragments such asFab′, Fab, F(ab)₂, single domain antibodies (DABs), Fv, scFv (singlechain Fv), and the like. The techniques for preparing and using variousantibody-based constructs and fragments are well known in the art. Meansfor preparing and characterizing antibodies are also well known in theart (See, e.g., Antibodies: A Laboratory Manual, Cold Spring HarborLaboratory, 1988; incorporated herein by reference).

The methods for generating monoclonal antibodies (MAbs) generally beginalong the same lines as those for preparing polyclonal antibodies.Briefly, a polyclonal antibody is prepared by immunizing an animal withan immunogenic NGVN composition in accordance with the present inventionand collecting antisera from that immunized animal.

A wide range of animal species can be used for the production ofantisera. Typically the animal used for production of antisera is arabbit, a mouse, a rat, a hamster, a guinea pig or a goat. Because ofthe relatively large blood volume of rabbits, a rabbit is a preferredchoice for production of polyclonal antibodies.

As is well known in the art, a given composition may vary in itsimmunogenicity. It is often necessary therefore to boost the host immunesystem, as may be achieved by coupling a peptide or polypeptideimmunogen to a carrier. Exemplary and preferred carriers are keyholelimpet hemocyanin (KLH) and bovine serum albumin (BSA). Other albuminssuch as ovalbumin, mouse serum albumin or rabbit serum albumin can alsobe used as carriers. Means for conjugating a polypeptide to a carrierprotein are well known in the art and include glutaraldehyde,m-maleimidobenzoyl-N-hydroxysuccinimide ester, carbodiimide andbis-biazotized benzidine.

As is also well known in the art, the immunogenicity of a particularimmunogen composition can be enhanced by the use of non-specificstimulators of the immune response, known as adjuvants. Suitableadjuvants include all acceptable immunostimulatory compounds, such ascytokines, toxins or synthetic compositions.

Adjuvants that may be used include IL-1, IL-2, IL-4, IL-7, IL-12,γ-interferon, GMCSP, BCG, aluminum hydroxide, MDP compounds, such asthur-MDP and nor-MDP, CGP (MTP-PE), lipid A, and monophosphoryl lipid A(MPL). RIBI, which contains three components extracted from bacteria,MPL, trehalose dimycolate (TDM) and cell wall skeleton (CWS) in a 2%squalene/Tween 80 emulsion is also contemplated. MHC antigens may evenbe used. Exemplary, often preferred adjuvants include complete Freund'sadjuvant (a non-specific stimulator of the immune response containingkilled Mycobacterium tuberculosis), incomplete Freund's adjuvants andaluminum hydroxide adjuvant.

In addition to adjuvants, it may be desirable to coadminister biologicresponse modifiers (BRM), which have been shown to upregulate T cellimmunity or downregulate suppressor cell activity. Such BRMs include,but are not limited to, Cimetidine (CIM; 1200 mg/d) (Smith/Kline, PA);low-dose Cyclophosphamide (CYP; 300 mg/m²) (Johnson/Mead, NJ), cytokinessuch as γ-interferon, IL-2, or IL-12 or genes encoding proteins involvedin immune helper functions, such as B-7.

The amount of immunogen composition used in the production of polyclonalantibodies varies upon the nature of the immunogen as well as the animalused for immunization. A variety of routes can be used to administer theimmunogen (subcutaneous, intramuscular, intradermal, intravenous andintraperitoneal). The production of polyclonal antibodies may bemonitored by sampling blood of the immunized animal at various pointsfollowing immunization.

A second, booster injection, may also be given. The process of boostingand titering is repeated until a suitable titer is achieved. When adesired level of immunogenicity is obtained, the immunized animal can bebled and the serum isolated and stored, and/or the animal can be used togenerate MAbs.

For production of rabbit polyclonal antibodies, the animal can be bledthrough an ear vein or alternatively by cardiac puncture. The removedblood is allowed to coagulate and then centrifuged to separate serumcomponents from whole cells and blood clots. The serum may be used as isfor various applications or else the desired antibody fraction may bepurified by well-known methods, such as affinity chromatography usinganother antibody, a peptide bound to a solid matrix, or by using, e.g.,protein A or protein G chromatography.

MAbs may be readily prepared through use of well-known techniques, suchas those exemplified in U.S. Pat. No. 4,196,265, incorporated herein byreference. Typically, this technique involves immunizing a suitableanimal with a selected immunogen composition, e.g., a purified orpartially purified NGVN protein, polypeptide, peptide or domain, be it awild-type or mutant composition. The immunizing composition isadministered in a manner effective to stimulate antibody producingcells.

The methods for generating monoclonal antibodies (MAbs) generally beginalong the same lines as those for preparing polyclonal antibodies.Rodents such as mice and rats are preferred animals, however, the use ofrabbit, sheep or frog cells is also possible. The use of rats mayprovide certain advantages (Goding, 1986, pp. 60-61), but mice arepreferred, with the BALB/c mouse being most preferred as this is mostroutinely used and generally gives a higher percentage of stablefusions.

The animals are injected with antigen, generally as described above. Theantigen may be coupled to carrier molecules such as keyhole limpethemocyanin if necessary. The antigen would typically be mixed withadjuvant, such as Freund's complete or incomplete adjuvant. Boosterinjections with the same antigen would occur at approximately two-weekintervals.

Following immunization, somatic cells with the potential for producingantibodies, specifically B lymphocytes (B cells), are selected for usein the MAb generating protocol. These cells may be obtained frombiopsied spleens, tonsils or lymph nodes, or from a peripheral bloodsample. Spleen cells and peripheral blood cells are preferred, theformer because they are a rich source of antibody-producing cells thatare in the dividing plasmablast stage, and the latter because peripheralblood is easily accessible.

Often, a panel of animals will have been immunized and the spleen of ananimal with the highest antibody titer will be removed and the spleenlymphocytes obtained by homogenizing the spleen with a syringe.Typically, a spleen from an immunized mouse contains approximately 5×10⁷to 2×10⁸ lymphocytes.

The antibody-producing B lymphocytes from the immunized animal are thenfused with cells of an immortal myeloma cell, generally one of the samespecies as the animal that was immunized. Myeloma cell lines suited foruse in hybridoma-producing fusion procedures preferably arenon-antibody-producing, have high fusion efficiency, and enzymedeficiencies that render then incapable of growing in certain selectivemedia which support the growth of only the desired fused cells(hybridomas).

Any one of a number of myeloma cells may be used, as are known to thoseof skill in the art (Goding, pp. 65-66, 1986; Campbell, 1984). Forexample, where the immunized animal is a mouse, one may use P3-X63/Ag8,X63-Ag8.653, NS1/1.Ag 4 1, Sp210-Ag14, FO, NSO/U, MPC-11, MCPC11-X45-GTG1.7 and S194/5XX0 Bul; for rats, one may use R210.RCY3, Y3-Ag 1.2.3,IR983F and 4B210; and U-266, GM1500-GRG2, LICR-LON-HMy2 and UC729-6 areall useful in connection with human cell fusions.

One preferred murine myeloma cell is the NS-1 myeloma cell line (alsotermed P3-NS-1-Ag4-1), which is readily available from the NIGMS HumanGenetic Mutant Cell Repository by requesting cell line repository numberGM3573. Another mouse myeloma cell line that may be used is the8-azaguanine-resistant mouse murine myeloma SP2/0 non-producer cellline.

Methods for generating hybrids of antibody-producing spleen or lymphnode cells and myeloma cells usually comprise mixing somatic cells withmyeloma cells in a 2:1 proportion, though the proportion may vary fromabout 20:1 to about 1:1, respectively, in the presence of an agent oragents (chemical or electrical) that promote the fusion of cellmembranes. Fusion methods using Sendai virus have been described byKohler and Milstein (1975; 1976), and those using polyethylene glycol(PEG), such as 37% (v/v) PEG, by Gefter et al. (1977). The use ofelectrically induced fusion methods is also appropriate (Goding pp.71-74, 1986).

Fusion procedures usually produce viable hybrids at low frequencies,about 1×10⁻⁶ to 1×10⁻⁸. However, this does not pose a problem, as theviable, fused hybrids are differentiated from the parental, unfusedcells (particularly the unfused myeloma cells that would normallycontinue to divide indefinitely) by culturing in a selective medium. Theselective medium is generally one that contains an agent that blocks thede novo synthesis of nucleotides in the tissue culture media. Exemplaryand preferred agents are aminopterin, methotrexate, and azaserine.Aminopterin and methotrexate block de novo synthesis of both purines andpyrimidines, whereas azaserine blocks only purine synthesis. Whereaminopterin or methotrexate is used, the media is supplemented withhypoxanthine and thymidine as a source of nucleotides (HAT medium).Where azaserine is used, the media is supplemented with hypoxanthine.

The preferred selection medium is HAT. Only cells capable of operatingnucleotide salvage pathways are able to survive in HAT medium. Themyeloma cells are defective in key enzymes of the salvage pathway, e.g.,hypoxanthine phosphoribosyl transferase (HPRT), and they cannot survive.The B cells can operate this pathway, but they have a limited life spanin culture and generally die within about two weeks. Therefore, the onlycells that can survive in the selective media are those hybrids formedfrom myeloma and B cells.

This culturing provides a population of hybridomas from which specifichybridomas are selected. Typically, selection of hybridomas is performedby culturing the cells by single-clone dilution in microtiter plates,followed by testing the individual clonal supernatants (after about twoto three weeks) for the desired reactivity. The assay should besensitive, simple and rapid, such as radioimmunoassays, enzymeimmunoassays, cytotoxicity assays, plaque assays, dot immunobindingassays, and the like.

The selected hybridomas would then be serially diluted and cloned intoindividual antibody-producing cell lines, which clones can then bepropagated indefinitely to provide MAbs. The cell lines may be exploitedfor MAb production in two basic ways. First, a sample of the hybridomacan be injected (often into the peritoneal cavity) into ahistocompatible animal of the type that was used to provide the somaticand myeloma cells for the original fusion (e.g., a syngeneic mouse).Optionally, the animals are primed with a hydrocarbon, especially oilssuch as pristane (tetramethylpentadecane) prior to injection. Theinjected animal develops tumors secreting the specific monoclonalantibody produced by the fused cell hybrid. The body fluids of theanimal, such as serum or ascites fluid, can then be tapped to provideMAbs in high concentration. Second, the individual cell lines could becultured in vitro, where the MAbs are naturally secreted into theculture medium from which they can be readily obtained in highconcentrations.

MAbs produced by either means may be further purified, if desired, usingfiltration, centrifugation and various chromatographic methods such asHPLC or affinity chromatography. Fragments of the monoclonal antibodiesof the invention can be obtained from the monoclonal antibodies soproduced by methods which include digestion with enzymes, such as pepsinor papain, and/or by cleavage of disulfide bonds by chemical reduction.Alternatively, monoclonal antibody fragments encompassed by the presentinvention can be synthesized using an automated peptide synthesizer.

It is also contemplated that a molecular cloning approach may be used togenerate monoclonals. For this, combinatorial immunoglobulin phagemidlibraries are prepared from RNA isolated from the spleen of theimmunized animal, and phagemids expressing appropriate antibodies areselected by panning using cells expressing the antigen and controlcells. The advantages of this approach over conventional hybridomatechniques are that approximately 10⁴ times as many antibodies can beproduced and screened in a single round, and that new specificities aregenerated by H and L chain combination which further increases thechance of finding appropriate antibodies.

Alternatively, monoclonal antibody fragments encompassed by the presentinvention can be synthesized using an automated peptide synthesizer, orby expression of full-length gene or of gene fragments in E. coli.

H. Antibody Conjugates

The present invention further provides antibodies against NGVN,generally of the monoclonal type, that are linked to one or more otheragents to form an antibody conjugate. Any antibody of sufficientselectivity, specificity and affinity may be employed as the basis foran antibody conjugate. Such properties may be evaluated usingconventional immunological screening methodology known to those of skillin the art.

Certain examples of antibody conjugates are those conjugates in whichthe antibody is linked to a detectable label. “Detectable labels” arecompounds or elements that can be detected due to their specificfunctional properties, or chemical characteristics, the use of whichallows the antibody to which they are attached to be detected, andfurther quantified if desired. Another such example is the formation ofa conjugate comprising an antibody linked to a cytotoxic oranti-cellular agent, as may be termed “immunotoxins” (described in U.S.Pat. Nos. 5,686,072, 5,578,706, 4,792,447, 5,045,451, 4,664,911 and5,767,072, each incorporated herein by reference).

Antibody conjugates are thus preferred for use as diagnostic agents.Antibody diagnostics generally fall within two classes, those for use inin vitro diagnostics, such as in a variety of immunoassays, and thosefor use in vivo diagnostic protocols, generally known as“antibody-directed imaging.” Again, antibody-directed imaging is lesspreferred for use with this invention.

Many appropriate imaging agents are known in the art, as are methods fortheir attachment to antibodies (see, e.g., U.S. Pat. Nos. 5,021,236 and4,472,509, both incorporated herein by reference). Certain attachmentmethods involve the use of a metal chelate complex employing, forexample, an organic chelating agent such a DTPA attached to the antibody(U.S. Pat. No. 4,472,509). Monoclonal antibodies may also be reactedwith an enzyme in the presence of a coupling agent such asglutaraldehyde or periodate. Conjugates with fluorescein markers areprepared in the presence of these coupling agents or by reaction with anisothiocyanate.

In the case of paramagnetic ions, one might mention by way of exampleions such as chromium (III), manganese (II), iron (III), iron (II),cobalt (II), nickel (II), copper (II), neodymium (III), samarium (III),ytterbium (III), gadolinium (III), vanadium (II), terbium (III),dysprosium (III), holmium (III) and erbium (III), with gadolinium beingparticularly preferred. Ions useful in other contexts, such as X-rayimaging, include but are not limited to lanthanum (III), gold (III),lead (II), and especially bismuth (III).

In the case of radioactive isotopes for therapeutic and/or diagnosticapplication, one might mention astatine²¹¹, ¹⁴carbon, ⁵¹chromium,³⁶chlorine, ⁵⁷cobalt, ⁵⁸cobalt, copper⁶⁷, ¹⁵²Eu, gallium⁶⁷, ³hydrogen,iodine¹²³, iodine¹²⁵, iodine¹³¹, indium¹¹¹, ⁵⁹iron, ³²phosphorus,rhenium¹⁸⁶, rhenium¹⁸⁸, ⁷⁵selenium, ³⁵sulphur, technicium^(99m) andyttrium⁹⁰. ¹²⁵I is often being preferred for use in certain embodiments,and technicium^(99m) and indium¹¹¹ are also often preferred due to theirlow energy and suitability for long range detection.

Radioactively labeled monoclonal antibodies of the present invention maybe produced according to well-known methods in the art. For instance,monoclonal antibodies can be iodinated by contact with sodium orpotassium iodide and a chemical oxidizing agent such as sodiumhypochlorite, or an enzymatic oxidizing agent, such as lactoperoxidase.Monoclonal antibodies according to the invention may be labeled withtechnetium-^(99m) by ligand exchange process, for example, by reducingpertechnate with stannous solution, chelating the reduced technetiumonto a Sephadex column and applying the antibody to this column or bydirect labeling techniques, e.g., by incubating pertechnate, a reducingagent such as SNCl₂, a buffer solution such as sodium-potassiumphthalate solution, and the antibody. Intermediary functional groupswhich are often used to bind radioisotopes which exist as metallic ionsto antibody are diethylenetriaminepentaacetic acid (DTPA) and ethylenediaminetetracetic acid (EDTA). Also contemplated for use are fluorescentlabels, including rhodamine, fluorescein isothiocyanate and renographin.

The much preferred antibody conjugates of the present invention arethose intended primarily for use in vitro, where the antibody is linkedto a secondary binding ligand or to an enzyme (an enzyme tag) that willgenerate a colored product upon contact with a chromogenic substrate.Examples of suitable enzymes include urease, alkaline phosphatase,(horseradish) hydrogen peroxidase and glucose oxidase. Preferredsecondary binding ligands are biotin and avidin or streptavidincompounds. The use of such labels is well known to those of skill in theart in light and is described, for example, in U.S. Pat. Nos. 3,817,837;3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149 and 4,366,241;each incorporated herein by reference.

2. NGVN Nucleic Acids

Important aspects of the present invention concern isolated DNA segmentsand recombinant vectors encoding NGVN proteins, polypeptides orpeptides, and the creation and use of recombinant host cells through theapplication of DNA technology, that express a wild-type, polymorphic ormutant NGVN, using the sequence of SEQ ID NO:1 and SEQ ID NO:3, andbiologically functional equivalents thereof.

The present invention concerns DNA segments, isolatable from mammaliancells, such as mouse, rat or human cells, that are free from totalgenomic DNA and that are capable of expressing a protein, polypeptide orpeptide. As used herein, the term “DNA segment” refers to a DNA moleculethat has been isolated free of total genomic DNA of a particularspecies. Therefore, a DNA segment encoding NGVN refers to a DNA segmentthat contains wild-type, polymorphic or mutant NGVN coding sequences yetis isolated away from, or purified free from, total mammalian genomicDNA. Included within the term “DNA segment”, are DNA segments andsmaller fragments of such segments, and also recombinant vectors,including, for example, plasmids, cosmids, phage, viruses, and the like.

Similarly, a DNA segment comprising an isolated or purified ngvn generefers to a DNA segment encoding NGVN protein, polypeptide or peptidecoding sequences and, in certain aspects, regulatory sequences, isolatedsubstantially away from other naturally-occurring genes or proteinencoding sequences. In this respect, the term “gene” is used forsimplicity to refer to a functional protein, polypeptide or peptideencoding unit. As will be understood by those in the art, thisfunctional term includes both genomic sequences, cDNA sequences andengineered segments that express, or may be adapted to express,proteins, polypeptides, domains, peptides, fusion proteins and mutantsof NGVN encoded sequences.

“Isolated substantially away from other coding sequences” means that thegene of interest, in this case the NGVN gene, forms the significant partof the coding region of the DNA segment, and that the DNA segment doesnot contain large portions of naturally-occurring coding DNA, such aslarge chromosomal fragments or other functional genes or cDNA codingregions. Of course, this refers to the DNA segment as originallyisolated, and does not exclude genes or coding regions later added tothe segment by the hand of man.

A. Variants

In particular embodiments, the invention concerns isolated DNA segmentsand recombinant vectors incorporating DNA sequences that encode a NGVNprotein, polypeptide or peptide that includes within its amino acidsequence a contiguous amino acid sequence in accordance with, oressentially as set forth in, SEQ ID NO:2, corresponding to the NGVNdesignated “human NGVN.”

The term “a sequence essentially as set forth in SEQ ID NO:2” means thatthe sequence substantially corresponds to a portion of SEQ ID NO:2 andhas relatively few amino acids that are not identical to, or abiologically functional equivalent of the amino acids of SEQ ID NO:2.

The term “biologically functional equivalent” is well understood in theart and is further defined in detail herein. Accordingly, sequences thathave about 70%, about 71%, about 72%, about 73%, about 74%, about 75%,about 76%, about 77%, about 78%, about 79%, about 80%, about 81%, about82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%,about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about95%, about 96%, about 97%, about 98%, or about 99%, and any rangederivable therein, such as, for example, about 70% to about 80%, andmore preferrably about 81% and about 90%; or even more preferably,between about 91% and about 99%; of amino acids that are identical orfunctionally equivalent to the amino acids of SEQ ID NO:2 will besequences that are “essentially as set forth in SEQ ID NO:2,” providedthe biological activity of the protein is maintained. In particularembodiments, the biological activity of a NGVN protein, polypeptide orpeptide, or a biologically functional equivalent, comprises binding toone or more proteases, particularly serine proteases. In specificembodiments, the biological activity of a NGVN protein, polypeptide orpeptide, or a biologically functional equivalent, comprises inhibitionof the activity of one or more proteases, particularly serine proteases,through binding. A preferred protease activity that may be inhibited bya NGVN protein, polypeptide or peptide, or a biologically functionalequivalent, is inhibition of the ability or rate of protealytic cleavagecatalyzed by the protease.

In certain other embodiments, the invention concerns isolated DNAsegments and recombinant vectors that include within their sequence anucleic acid sequence essentially as set forth in SEQ ID NO:1. The term“essentially as set forth in SEQ ID NO:1” is used in the same sense asdescribed above and means that the nucleic acid sequence substantiallycorresponds to a portion of SEQ ID NO:1 and has relatively few codonsthat are not identical, or functionally equivalent, to the codons of SEQID NO:1.

The term “functionally equivalent codon” is used herein to refer tocodons that encode the same amino acid, such as the six codons forarginine and serine, and also refers to codons that encode biologicallyequivalent amino acids. For optimization of expression of NGVN in humancells, the codons are shown in Table 1 in preference of use from left toright. Thus, the most preferred codon for alanine is thus “GCC”, and theleast is “GCG” (see Table 1 below). Codon usage for various organismsand organelles can be found at the websitehttp://www.kazusa.or.jp/codon/, incorporated herein by reference,allowing one of skill in the art to optimize codon usage for expressionin various organisms using the disclosures herein. Thus, it iscontemplated that codon usage may be optimized for other animals, aswell as other organisms such as a prokaryote (e.g., an eubacteria, anarchaea), an eukaryote (e.g., a protist, a plant, a fungi, an animal), avirus and the like, as well as organelles that contain nucleic acids,such as mitochondria or chloroplasts, based on the preferred codon usageas would be known to those of ordinary skill in the art.

TABLE 1 Preferred Human DNA Codons Amino Acids Codons Alanine Ala A GCCGCT GCA GCG Cysteine Cys C TGC TGT Aspartic acid Asp D GAC GATGlutamic acid Glu E GAG GAA Phenylalanine Phe F TTC TTT Glycine Gly GGGC GGG GGA GGT Histidine His H CAC CAT Isoleucine Ile I ATC ATT ATALysine Lys K AAG AAA Leucine Leu L CTG CTC TTG CTT CTA TTA MethionineMet M ATG Asparagine Asn N AAC AAT Proline Pro P CCC CCT CCA CCGGlutamine Gln Q CAG CAA Arginine Arg R CGC AGG CGG AGA CGA CGT SerineSer S AGC TCC TCT AGT TCA TCG Threonine Thr T ACC ACA ACT ACG Valine ValV GTG GTC GTT GTA Tryptophan Trp W TGG Tyrosine Tyr Y TAC TAT

It will also be understood that amino acid and nucleic acid sequencesmay include additional residues, such as additional N- or C-terminalamino acids or 5′ or 3′ sequences, and yet still be essentially as setforth in one of the sequences disclosed herein, so long as the sequencemeets the criteria set forth above, including the maintenance ofbiological protein, polypeptide or peptide activity where an amino acidsequence expression is concerned. The addition of terminal sequencesparticularly applies to nucleic acid sequences that may, for example,include various non-coding sequences flanking either of the 5′ or 3′portions of the coding region or may include various internal sequences,i.e., introns, which are known to occur within genes.

Excepting intronic or flanking regions, and allowing for the degeneracyof the genetic code, sequences that have about 70%, about 71%, about72%, about 73%, about 74%, about 75%, about 76%, about 77%, about 78%,about 79%, about 80%, about 81%, about 82%, about 83%, about 84%, about85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%,about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about98%, or about 99%, and any range derivable therein, such as, forexample, about 70% to about 80%, and more preferrably about 81% andabout 90%; or even more preferably, between about 91% and about 99%; ofnucleotides that are identical to the nucleotides of SEQ ID NO:1 or NO:3will be sequences that are “essentially as set forth in SEQ ID NO:1 orNO:3.”

B. Nucleic Acid Hybidization

The nucleic acid sequences disclosed herein also have a variety of uses,such as for example, utility as probes or primers in nucleic acidhybridization embodiments.

Naturally, the present invention also encompasses DNA segments that arecomplementary, or essentially complementary, to the sequence set forthin SEQ ID NO:1 and NO:3. Nucleic acid sequences that are “complementary”are those that are capable of base-pairing according to the standardWatson-Crick complementarity rules. As used herein, the term“complementary sequences” means nucleic acid sequences that aresubstantially complementary, as may be assessed by the same nucleotidecomparison set forth above, or as defined as being capable ofhybridizing to the nucleic acid segment of SEQ ID NO:1 and NO:3 understringent conditions such as those described herein.

As used herein, “hybridization”, “hybridizes” or “capable ofhybridizing” is understood to mean the forming of a double or triplestranded molecule or a molecule with partial double or triple strandednature. The term “hybridization”, “hybridize(s)” or “capable ofhybridizing” encompasses the terms “stringent condition(s)” or “highstringency” and the terms “low stringency” or “low stringencycondition(s).”

As used herein “stringent condition(s)” or “high stringency” are thoseconditions that allow hybridization between or within one or morenucleic acid strand(s) containing complementary sequence(s), butprecludes hybridization of random sequences. Stringent conditionstolerate little, if any, mismatch between a nucleic acid and a targetstrand. Such conditions are well known to those of ordinary skill in theart, and are preferred for applications requiring high selectivity.Non-limiting applications include isolating a nucleic acid, such as agene or a nucleic acid segment thereof, or detecting at least onespecific mRNA transcript or a nucleic acid segment thereof, and thelike.

Stringent conditions may comprise low salt and/or high temperatureconditions, such as provided by about 0.02 M to about 0.15 M NaCl attemperatures of about 50° C. to about 70° C. It is understood that thetemperature and ionic strength of a desired stringency are determined inpart by the length of the particular nucleic acid(s), the length andnucleobase content of the target sequence(s), the charge composition ofthe nucleic acid(s), and to the presence or concentration of formamide,tetramethylammonium chloride or other solvent(s) in a hybridizationmixture.

It is also understood that these ranges, compositions and conditions forhybridization are mentioned by way of non-limiting examples only, andthat the desired stringency for a particular hybridization reaction isoften determined empirically by comparison to one or more positive ornegative controls. Depending on the application envisioned it ispreferred to employ varying conditions of hybridization to achievevarying degrees of selectivity of a nucleic acid towards a targetsequence. In a non-limiting example, identification or isolation of arelated target nucleic acid that does not hybridize to a nucleic acidunder stringent conditions may be achieved by hybridization at lowtemperature and/or high ionic strength. For example, a medium stringencycondition could be provided by about 0.1 to 0.25 M NaCl at temperaturesof about 37° C. to about 55° C. Under these conditions, hybridizationmay occur even though the sequences of probe and target strand are notperfectly complementary, but are mismatched at one or more positions. Inanother example, a low stringency condition could be provided by about0.15 M to about 0.9 M salt, at temperatures ranging from about 20° C. toabout 55° C. Of course, it is within the skill of one in the art tofurther modify the low or high stringency conditions to suite aparticular application. For example, in other embodiments, hybridizationmay be achieved under conditions of, 50 mM Tris-HCl (pH 8.3), 75 mM KCl,3 mM MgCl₂, 1.0 mM dithiothreitol, at temperatures between approximately20° C. to about 37° C. Other hybridization conditions utilized couldinclude approximately 10 mM Tris-HCl (pH 8.3), 50 mM KCl, 1.5 mM MgCl₂,at temperatures ranging from approximately 40° C. to about 72° C.

Accordingly, the nucleotide sequences of the disclosure may be used fortheir ability to selectively form duplex molecules with complementarystretches of genes or RNAs or to provide primers for amplification ofDNA or RNA from tissues. Depending on the application envisioned, it ispreferred to employ varying conditions of hybridization to achievevarying degrees of selectivity of probe towards target sequence.

The nucleic acid segments of the present invention, regardless of thelength of the coding sequence itself, may be combined with other DNAsequences, such as promoters, enhancers, polyadenylation signals,additional restriction enzyme sites, multiple cloning sites, othercoding segments, and the like, such that their overall length may varyconsiderably. It is therefore contemplated that a nucleic acid fragmentof almost any length may be employed, with the total length preferablybeing limited by the ease of preparation and use in the intendedrecombinant DNA protocol.

For example, nucleic acid fragments may be prepared that include acontiguous stretch of nucleotides identical to or complementary to SEQID NO:1 or NO:3, such as, for example, about 8, about 10 to about 14, orabout 15 to about 20 nucleotides, and that are chromosome sized pieces,up to about 1,000,000, about 750,000, about 500,000, about 250,000,about 100,000, about 50,000, about 20,000, or about 10,000, or about5,000 base pairs in length, with segments of about 3,000 being preferredin certain cases, as well as DNA segments with total lengths of about1,000, about 500, about 200, about 100 and about 50 base pairs in length(including all intermediate lengths of these lengths listed above, i.e.,any range derivable therein and any integer derivable therein such arange) are also contemplated to be useful.

For example, it will be readily understood that “intermediate lengths”,in these contexts, means any length between the quoted ranges, such as10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 65, 70, 75,80, 85, 90, 95, 100, 105, 110, 115, 120, 130, 140, 150, 160, 170, 180,190, including all integers through the 200-500; 500-1,000; 1,000-2,000;2,000-3,000; 3,000-5,000; 5,000-10,000 ranges, up to and includingsequences of about 12,001, 12,002, 13,001, 13,002, 15,000, 20,000 andthe like.

Various nucleic acid segments may be designed based on a particularnucleic acid sequence, and may be of any length. By assigning numericvalues to a sequence, for example, the first residue is 1, the secondresidue is 2, etc., an algorithm defining all nucleic acid segments canbe created:

-   -   n to n+y        where n is an integer from 1 to the last number of the sequence        and y is the length of the nucleic acid (SEQ ID NO:1 and NO:3)        segment minus one, where n+y does not exceed the last number of        the sequence. Thus, for a 10-mer, the nucleic acid segments        correspond to bases 1 to 10, 2 to 11, 3 to 12 . . . and/or so        on. For a 15-mer, the nucleic acid segments correspond to bases        1 to 15, 2 to 16, 3 to 17 . . . and/or so on. For a 20-mer, the        nucleic segments correspond to bases 1 to 20, 2 to 21, 3 to 22 .        . . and/or so on. In certain embodiments, the nucleic acid        segment may be a probe or primer. As used herein, a “probe”        generally refers to a nucleic acid used in a detection method or        composition. As used herein, a “primer” generally refers to a        nucleic acid used in an extension or amplification method or        composition.

The use of a hybridization probe of between 17 and 100 nucleotides inlength, or in some aspect of the invention even up to 1-2 kb or more inlength, allows the formation of a duplex molecule that is both stableand selective. Molecules having complementary sequences over stretchesgreater than 20 bases in length are generally preferred, in order toincrease stability and selectivity of the hybrid, and thereby improvethe quality and degree of particular hybrid molecules obtained. One willgenerally prefer to design nucleic acid molecules having stretches of 20to 30 nucleotides, or even longer where desired. Such fragments may bereadily prepared by, for example, directly synthesizing the fragment bychemical means or by introducing selected sequences into recombinantvectors for recombinant production.

In general, it is envisioned that the hybridization probes describedherein will be useful both as reagents in solution hybridization, as inPCR™, for detection of expression of corresponding genes, as well as inembodiments employing a solid phase. In embodiments involving a solidphase, the test DNA (or RNA) is adsorbed or otherwise affixed to aselected matrix or surface. This fixed, single-stranded nucleic acid isthen subjected to hybridization with selected probes under desiredconditions. The selected conditions will depend on the particularcircumstances based on the particular criteria required (depending, forexample, on the “G+C” content, type of target nucleic acid, source ofnucleic acid, size of hybridization probe, etc.). Following washing ofthe hybridized surface to remove non-specifically bound probe molecules,hybridization is detected, or even quantified, by means of the label.

C. Nucleic Acid Amplification

Nucleic acid used as a template for amplification is isolated from cellscontained in the biological sample, according to standard methodologies(Sambrook et al., 1989). The nucleic acid may be genomic DNA orfractionated or whole cell RNA. Where RNA is used, it may be desired toconvert the RNA to a complementary DNA. In one embodiment, the RNA iswhole cell RNA and is used directly as the template for amplification.

Pairs of primers that selectively hybridize to nucleic acidscorresponding to NGVN genes are contacted with the isolated nucleic acidunder conditions that permit selective hybridization. The term “primer,”as defined herein, is meant to encompass any nucleic acid that iscapable of priming the synthesis of a nascent nucleic acid in atemplate-dependent process. Typically, primers are oligonucleotides fromten to twenty or thirty base pairs in length, but longer sequences canbe employed. Primers may be provided in double-stranded orsingle-stranded form, although the single-stranded form is preferred.

Once hybridized, the nucleic acid:primer complex is contacted with oneor more enzymes that facilitate template-dependent nucleic acidsynthesis. Multiple rounds of amplification, also referred to as“cycles,” are conducted until a sufficient amount of amplificationproduct is produced.

Next, the amplification product is detected. In certain applications,the detection may be performed by visual means. Alternatively, thedetection may involve indirect identification of the product viachemiluminescence, radioactive scintigraphy of incorporated radiolabelor fluorescent label or even via a system using electrical or thermalimpulse signals (Affymax technology).

A number of template dependent processes are available to amplify themarker sequences present in a given template sample. One of the bestknown amplification methods is the polymerase chain reaction (referredto as PCR™) which is described in detail in U.S. Pat. Nos. 4,683,195,4,683,202 and 4,800,159, each incorporated herein by reference inentirety.

Briefly, in PCR™, two primer sequences are prepared that arecomplementary to regions on opposite complementary strands of the markersequence. An excess of deoxynucleoside triphosphates are added to areaction mixture along with a DNA polymerase, e.g., Taq polymerase. Ifthe marker sequence is present in a sample, the primers will bind to themarker and the polymerase will cause the primers to be extended alongthe marker sequence by adding on nucleotides. By raising and loweringthe temperature of the reaction mixture, the extended primers willdissociate from the marker to form reaction products, excess primerswill bind to the marker and to the reaction products and the process isrepeated.

A reverse transcriptase PCR amplification procedure may be performed inorder to quantify the amount of mRNA amplified. Methods of reversetranscribing RNA into cDNA are well known and described in Sambrook etal., 1989. Alternative methods for reverse transcription utilizethermostable, RNA-dependent DNA polymerases. These methods are describedin WO 90/07641, filed Dec. 21, 1990, incorporated herein by reference.Polymerase chain reaction methodologies are well known in the art.

Another method for amplification is the ligase chain reaction (“LCR”),disclosed in EPA No. 320 308, incorporated herein by reference in itsentirety. In LCR, two complementary probe pairs are prepared, and in thepresence of the target sequence, each pair will bind to oppositecomplementary strands of the target such that they abut. In the presenceof a ligase, the two probe pairs will link to form a single unit. Bytemperature cycling, as in PCR™, bound ligated units dissociate from thetarget and then serve as “target sequences” for ligation of excess probepairs. U.S. Pat. No. 4,883,750 describes a method similar to LCR forbinding probe pairs to a target sequence.

Qbeta Replicase, described in PCT Application No. PCT/US87/00880,incorporated herein by reference, may also be used as still anotheramplification method in the present invention. In this method, areplicative sequence of RNA that has a region complementary to that of atarget is added to a sample in the presence of an RNA polymerase. Thepolymerase will copy the replicative sequence that can then be detected.

An isothermal amplification method, in which restriction endonucleasesand ligases are used to achieve the amplification of target moleculesthat contain nucleotide 5′-[alpha-thio]-triphosphates in one strand of arestriction site may also be useful in the amplification of nucleicacids in the present invention.

Strand Displacement Amplification (SDA) is another method of carryingout isothermal amplification of nucleic acids which involves multiplerounds of strand displacement and synthesis, i.e., nick translation. Asimilar method, called Repair Chain Reaction (RCR), involves annealingseveral probes throughout a region targeted for amplification, followedby a repair reaction in which only two of the four bases are present.The other two bases can be added as biotinylated derivatives for easydetection. A similar approach is used in SDA. Target specific sequencescan also be detected using a cyclic probe reaction (CPR). In CPR, aprobe having 3′ and 5′ sequences of non-specific DNA and a middlesequence of specific RNA is hybridized to DNA that is present in asample. Upon hybridization, the reaction is treated with RNase H, andthe products of the probe identified as distinctive products that arereleased after digestion. The original template is annealed to anothercycling probe and the reaction is repeated.

Still another amplification methods described in GB Application No. 2202 328, and in PCT Application No. PCT/US89/01025, each of which isincorporated herein by reference in its entirety, may be used inaccordance with the present invention. In the former application,“modified” primers are used in a PCR-like, template- andenzyme-dependent synthesis. The primers may be modified by labeling witha capture moiety (e.g., biotin) and/or a detector moiety (e.g., enzyme).In the latter application, an excess of labeled probes are added to asample. In the presence of the target sequence, the probe binds and iscleaved catalytically. After cleavage, the target sequence is releasedintact to be bound by excess probe. Cleavage of the labeled probesignals the presence of the target sequence.

Other nucleic acid amplification procedures include transcription-basedamplification systems (TAS), including nucleic acid sequence basedamplification (NASBA) and 3SR (Gingeras et al., PCT Application WO88/10315, incorporated herein by reference). In NASBA, the nucleic acidscan be prepared for amplification by standard phenol/chloroformextraction, heat denaturation of a clinical sample, treatment with lysisbuffer and minispin columns for isolation of DNA and RNA or guanidiniumchloride extraction of RNA. These amplification techniques involveannealing a primer which has target specific sequences. Followingpolymerization, DNA/RNA hybrids are digested with RNase H while doublestranded DNA molecules are heat denatured again. In either case thesingle stranded DNA is made fully double stranded by addition of secondtarget specific primer, followed by polymerization. The double-strandedDNA molecules are then multiply transcribed by an RNA polymerase such asT7 or SP6. In an isothermal cyclic reaction, the RNA's are reversetranscribed into single stranded DNA, which is then converted to doublestranded DNA, and then transcribed once again with an RNA polymerasesuch as T7 or SP6. The resulting products, whether truncated orcomplete, indicate target specific sequences.

Davey et al., EP 329 822 (incorporated herein by reference in itsentirety) disclose a nucleic acid amplification process involvingcyclically synthesizing single-stranded RNA (“ssRNA”), ssDNA, anddouble-stranded DNA (dsDNA), which may be used in accordance with thepresent invention. The ssRNA is a template for a first primeroligonucleotide, which is elongated by reverse transcriptase(RNA-dependent DNA polymerase). The RNA is then removed from theresulting DNA:RNA duplex by the action of ribonuclease H(RNase H, anRNase specific for RNA in duplex with either DNA or RNA). The resultantssDNA is a template for a second primer, which also includes thesequences of an RNA polymerase promoter (exemplified by T7 RNApolymerase) 5′ to its homology to the template. This primer is thenextended by DNA polymerase (exemplified by the large “Klenow” fragmentof E. coli DNA polymerase I), resulting in a double-stranded DNA(“dsDNA”) molecule, having a sequence identical to that of the originalRNA between the primers and having additionally, at one end, a promotersequence. This promoter sequence can be used by the appropriate RNApolymerase to make many RNA copies of the DNA. These copies can thenre-enter the cycle leading to very swift amplification. With properchoice of enzymes, this amplification can be done isothermally withoutaddition of enzymes at each cycle. Because of the cyclical nature ofthis process, the starting sequence can be chosen to be in the form ofeither DNA or RNA.

Miller et al., PCT Application WO 89/06700 (incorporated herein byreference in its entirety) disclose a nucleic acid sequenceamplification scheme based on the hybridization of a promoter/primersequence to a target single-stranded DNA (“ssDNA”) followed bytranscription of many RNA copies of the sequence. This scheme is notcyclic, i.e., new templates are not produced from the resultant RNAtranscripts. Other amplification methods include “RACE” and “one=sidedPCR” (Frohman, 1990, incorporated herein by reference).

Methods based on ligation of two (or more) oligonucleotides in thepresence of nucleic acid having the sequence of the resulting“di-oligonucleotide”, thereby amplifying the di-oligonucleotide, mayalso be used in the amplification step of the present invention.

D. Nucleic Acid Detection

In certain embodiments, it will be advantageous to employ nucleic acidsequences of the present invention in combination with an appropriatemeans, such as a label, for determining hybridization. A wide variety ofappropriate indicator means are known in the art, including fluorescent,radioactive, enzymatic or other ligands, such as avidin/biotin, whichare capable of being detected. In preferred embodiments, one may desireto employ a fluorescent label or an enzyme tag such as urease, alkalinephosphatase or peroxidase, instead of radioactive or otherenvironmentally undesirable reagents. In the case of enzyme tags,colorimetric indicator substrates are known that can be employed toprovide a detection means visible to the human eye orspectrophotometrically, to identify specific hybridization withcomplementary nucleic acid-containing samples.

In embodiments wherein nucleic acids are amplified, it may be desirableto separate the amplification product from the template and the excessprimer for the purpose of determining whether specific amplification hasoccurred. In one embodiment, amplification products are separated byagarose, agarose-acrylamide or polyacrylamide gel electrophoresis usingstandard methods (Sambrook et al., 1989).

Alternatively, chromatographic techniques may be employed to effectseparation. There are many kinds of chromatography which may be used inthe present invention: adsorption, partition, ion-exchange and molecularsieve, and many specialized techniques for using them including column,paper, thin-layer and gas chromatography.

Amplification products must be visualized in order to confirmamplification of the marker sequences. One typical visualization methodinvolves staining of a gel with ethidium bromide and visualization underUV light. Alternatively, if the amplification products are integrallylabeled with radio- or fluorometrically-labeled nucleotides, theamplification products can then be exposed to x-ray film or visualizedunder the appropriate stimulating spectra, following separation.

In one embodiment, visualization is achieved indirectly. Followingseparation of amplification products, a labeled, nucleic acid probe isbrought into contact with the amplified marker sequence. The probepreferably is conjugated to a chromophore but may be radiolabeled. Inanother embodiment, the probe is conjugated to a binding partner, suchas an antibody or biotin, and the other member of the binding paircarries a detectable moiety.

In one embodiment, detection is by Southern blotting and hybridizationwith a labeled probe. The techniques involved in Southern blotting arewell known to those of skill in the art and can be found in manystandard books on molecular protocols (See Sambrook et al., 1989).Briefly, amplification products are separated by gel electrophoresis.The gel is then contacted with a membrane, such as nitrocellulose,permitting transfer of the nucleic acid and non-covalent binding.Subsequently, the membrane is incubated with a chromophore-conjugatedprobe that is capable of hybridizing with a target amplificationproduct. Detection is by exposure of the membrane to x-ray film orion-emitting detection devices.

One example of the foregoing is described in U.S. Pat. No. 5,279,721,incorporated by reference herein, which discloses an apparatus andmethod for the automated electrophoresis and transfer of nucleic acids.The apparatus permits electrophoresis and blotting without externalmanipulation of the gel and is ideally suited to carrying out methodsaccording to the present invention.

Other methods for genetic screening to accurately detect mutations ingenomic DNA, cDNA or RNA samples may be employed, depending on thespecific situation.

Historically, a number of different methods have been used to detectpoint mutations, including denaturing gradient gel electrophoresis(“DGGE”), restriction enzyme polymorphism analysis, chemical andenzymatic cleavage methods, and others. The more common procedurescurrently in use include direct sequencing of target regions amplifiedby PCR™ (see above) and single-strand conformation polymorphism analysis(“SSCP”).

Another method of screening for point mutations is based on RNasecleavage of base pair mismatches in RNA/DNA and RNA/RNA heteroduplexes.As used herein, the term “mismatch” is defined as a region of one ormore unpaired or mispaired nucleotides in a double-stranded RNA/RNA,RNA/DNA or DNA/DNA molecule. This definition thus includes mismatchesdue to insertion/deletion mutations, as well as single and multiple basepoint mutations.

U.S. Pat. No. 4,946,773 describes an RNase A mismatch cleavage assaythat involves annealing single-stranded DNA or RNA test samples to anRNA probe, and subsequent treatment of the nucleic acid duplexes withRNase A. After the RNase cleavage reaction, the RNase is inactivated byproteolytic digestion and organic extraction, and the cleavage productsare denatured by heating and analyzed by electrophoresis on denaturingpolyacrylamide gels. For the detection of mismatches, thesingle-stranded products of the RNase A treatment, electrophoreticallyseparated according to size, are compared to similarly treated controlduplexes. Samples containing smaller fragments (cleavage products) notseen in the control duplex are scored as positive.

Currently available RNase mismatch cleavage assays, including thoseperformed according to U.S. Pat. No. 4,946,773, require the use ofradiolabeled RNA probes. Myers and Maniatis in U.S. Pat. No. 4,946,773describe the detection of base pair mismatches using RNase A. Otherinvestigators have described the use of an E. coli enzyme, RNase I, inmismatch assays. Because it has broader cleavage specificity than RNaseA, RNase I would be a desirable enzyme to employ in the detection ofbase pair mismatches if components can be found to decrease the extentof non-specific cleavage and increase the frequency of cleavage ofmismatches. The use of RNase I for mismatch detection is described inliterature from Promega Biotech. Promega markets a kit containing RNaseI that is shown in their literature to cleave three out of four knownmismatches, provided the enzyme level is sufficiently high.

The RNase protection assay was first used to detect and map the ends ofspecific mRNA targets in solution. The assay relies on being able toeasily generate high specific activity radiolabeled RNA probescomplementary to the mRNA of interest by in vitro transcription.Originally, the templates for in vitro transcription were recombinantplasmids containing bacteriophage promoters. The probes are mixed withtotal cellular RNA samples to permit hybridization to theircomplementary targets, then the mixture is treated with RNase to degradeexcess unhybridized probe. Also, as originally intended, the RNase usedis specific for single-stranded RNA, so that hybridized double-strandedprobe is protected from degradation. After inactivation and removal ofthe RNase, the protected probe (which is proportional in amount to theamount of target mRNA that was present) is recovered and analyzed on apolyacrylamide gel.

The RNase Protection assay was adapted for detection of single basemutations. In this type of RNase A mismatch cleavage assay, radiolabeledRNA probes transcribed in vitro from wild-type sequences, are hybridizedto complementary target regions derived from test samples. The testtarget generally comprises DNA (either genomic DNA or DNA amplified bycloning in plasmids or by PCR™), although RNA targets (endogenous mRNA)have occasionally been used. If single nucleotide (or greater) sequencedifferences occur between the hybridized probe and target, the resultingdisruption in Watson-Crick hydrogen bonding at that position(“mismatch”) can be recognized and cleaved in some cases bysingle-strand specific ribonuclease. To date, RNase A has been usedalmost exclusively for cleavage of single-base mismatches, althoughRNase I has recently been shown as useful also for mismatch cleavage.There are recent descriptions of using the MutS protein and otherDNA-repair enzymes for detection of single-base mismatches.

E. Cloning of Additional NGVN Genes

The present invention contemplates cloning NGVN genes or cDNAs fromanimal (e.g., mammalian) organisms. A technique often employed by thoseskilled in the art of protein production today is to obtain a so-called“recombinant” version of the protein, to express it in a recombinantcell and to obtain the protein, polypeptide or peptide from such cells.These techniques are based upon the “cloning” of a DNA molecule encodingthe protein from a DNA library, i.e., on obtaining a specific DNAmolecule distinct from other portions of DNA. This can be achieved by,for example, cloning a cDNA molecule, or cloning a genomic-like DNAmolecule.

The first step in such cloning procedures is the screening of anappropriate DNA library. The screening protocol may utilize nucleotidesegments or probes derived from SEQ ID NOS:1 or 3. Additionally,antibodies designed to bind to the expressed NGVN proteins,polypeptides, or peptides may be used as probes to screen an appropriatemammalian DNA expression library. Alternatively, activity assays may beemployed. The operation of such screening protocols are well known tothose of skill in the art and are described in detail in the scientificliterature, for example, in Sambrook et al. (1989), incorporated hereinby reference. Moreover, as the present invention encompasses the cloningof genomic segments as well as cDNA molecules, it is contemplated thatsuitable genomic cloning methods, as known to those in the art, may alsobe used.

As used herein “designed to hybridize” means a sequence selected for itslikely ability to hybridize to a mammalian NGVN gene, for example due tothe expected high degree of homology between the human, rat, or mouseNGVN gene and the NGVN genes from other mammals. Also included aresegments or probes altered to enhance their ability to hybridize to orbind to a mammalian NGVN gene. Additionally, these regions of homologyalso include amino acid sequences of 4 or more consecutive amino acidsselected and/or altered to increase conservation of the amino acidsequences in comparison to the same or similar region of residues in thesame or related genes in one or more species. Such amino acid sequencesmay derived from amino acid sequences encoded by the NGVN gene, and moreparticularly from the isolated sequences of SEQ ID NO:2.

Designing probe sequences may involve selection of regions of highlyconserved nucleotide sequences between various species for a particulargene or related genes, relative to the general conservation ofnucleotides of the gene or related genes in one or more species.Comparison of the amino acid sequences conserved between one or morespecies for a particular gene may also be used to determine a group of 4or more consecutive amino acids that are conserved relative to theprotein encoded by the gene or related genes. The nucleotide probe orprimers may then be designed from the region of the gene that encodesthe conserved sequence of amino acids.

One may also prepare fusion proteins, polypeptides and peptides, e.g.,where the NGVN proteinaceous material coding regions are aligned withinthe same expression unit with other proteins, polypeptides or peptideshaving desired functions, such as for purification or immunodetectionpurposes (e.g., proteinaceous compostions that may be purified byaffinity chromatography and enzyme label coding regions, respectively).

Encompassed by the invention are DNA segments encoding relatively smallpeptides, such as, for example, peptides of from about 8, about 9, about10, about 11, about 12, about 13, about 14, about 15, about 16, about17, about 18, about 19, about 20, about 21, about 22, about 23, about24, about 25, about 26, about 27, about 28, about 29, about 30, about31, about 32, about 33, about 34, about 35, about 35, about 40, about45, to about 50 amino acids in length, and more preferably, of fromabout 15 to about 30 amino acids in length; as set forth in SEQ ID NO:2and also larger polypeptides up to and including proteins correspondingto the full-length sequences set forth in SEQ ID NO:2, and any rangederivable therein and any integer derivable therein such a range.

In addition to the “standard” DNA and RNA nucleotide bases, modifiedbases are also contemplated for use in particular applications of thepresent invention. A table of exemplary, but not limiting, modifiedbases is provided herein below.

TABLE 2 Modified Bases Abbr. Modified base description ac4c4-acetylcytidine chm5u 5-(carboxyhydroxylmethyl)uridine Cm2′-O-methylcytidine Cmnm5s2u 5-carboxymethylaminomethyl-2-thioridineCmnm5u 5-carboxymethylaminomethyluridine D Dihydrouridine Fm2′-O-methylpseudouridine gal q Beta,D-galactosylqueosine Gm2′-O-methylguanosine I Inosine I6a N6-isopentenyladenosine m1a1-methyladenosine m1f 1-methylpseudouridine m1g 1-methylguanosine m1I1-methylinosine m22g 2,2-dimethylguanosine m2a 2-methyladenosine m2g2-methylguanosine m3c 3-methylcytidine m5c 5-methylcytidine m6aN6-methyladenosine m7g 7-methylguanosine Mam5u5-methylaminomethyluridine Mam5s2u 5-methoxyaminomethyl-2-thiouridineMan q Beta,D-mannosylqueosine Mcm5s2u5-methoxycarbonylmethyl-2-thiouridine Mcm5u5-methoxycarbonylmethyluridine Mo5u 5-methoxyuridine Ms2i6a2-methylthio-N6-isopentenyladenosine Ms2t6aN-((9-beta-D-ribofuranosyl-2- methylthiopurine-6-yl)carbamoyl)threonineMt6a N-((9-beta-D-ribofuranosylpurine-6-yl)N- methyl-carbamoyl)threonineMv Uridine-5-oxyacetic acid methylester o5u Uridine-5-oxyacetic acid (v)Osyw Wybutoxosine P Pseudouridine Q Queosine s2c 2-thiocytidine s2t5-methyl-2-thiouridine s2u 2-thiouridine s4u 4-thiouridine T5-methyluridine t6a N-((9-beta-D-ribofuranosylpurine-6-yl)carbamoyl)threonine Tm 2′-O-methyl-5-methyluridine Um2′-O-methyluridine Yw Wybutosine X3-(3-amino-3-carboxypropyl)uridine,(acp3)u

F. Mutagenesis, Peptidomimetics and Rational Drug Design

It will also be understood that this invention is not limited to theparticular nucleic acid and amino acid sequences of SEQ ID NO:2.Recombinant vectors and isolated DNA segments may therefore variouslyinclude these coding regions themselves, coding regions bearing selectedalterations or modifications in the basic coding region, or they mayencode larger polypeptides that nevertheless include such coding regionsor may encode biologically functional equivalent proteins, polypeptidesor peptides that have variant amino acids sequences.

The DNA segments of the present invention encompass biologicallyfunctional equivalent NGVN proteins, polypeptides, and peptides. Suchsequences may arise as a consequence of codon redundancy and functionalequivalency that are known to occur naturally within nucleic acidsequences and the proteinaceous compositions thus encoded.Alternatively, functionally equivalent proteins, polypeptides orpeptides may be created via the application of recombinant DNAtechnology, in which changes in the protein, polypeptide or peptidestructure may be engineered, based on considerations of the propertiesof the amino acids being exchanged. Changes may be introduced, forexample, through the application of site-directed mutagenesis techniquesas discussed herein below, e.g., to introduce improvements to theantigenicity of the proteinaceous composition or to test mutants inorder to examine NGVN activity at the molecular level.

Site-specific mutagenesis is a technique useful in the preparation ofindividual peptides, or biologically functional equivalent proteins,polypeptides or peptides, through specific mutagenesis of the underlyingDNA. The technique further provides a ready ability to prepare and testsequence variants, incorporating one or more of the foregoingconsiderations, by introducing one or more nucleotide sequence changesinto the DNA. Site-specific mutagenesis allows the production of mutantsthrough the use of specific oligonucleotide sequences which encode theDNA sequence of the desired mutation, as well as a sufficient number ofadjacent nucleotides, to provide a primer sequence of sufficient sizeand sequence complexity to form a stable duplex on both sides of thedeletion junction being traversed. Typically, a primer of about 17 to 25nucleotides in length is preferred, with about 5 to 10 residues on bothsides of the junction of the sequence being altered.

In general, the technique of site-specific mutagenesis is well known inthe art. As will be appreciated, the technique typically employs abacteriophage vector that exists in both a single stranded and doublestranded form. Typical vectors useful in site-directed mutagenesisinclude vectors such as the M13 phage. These phage vectors arecommercially available and their use is generally well known to thoseskilled in the art. Double-stranded plasmids are also routinely employedin site directed mutagenesis, which eliminates the step of transferringthe gene of interest from a phage to a plasmid.

In general, site-directed mutagenesis is performed by first obtaining asingle-stranded vector, or melting of two strands of a double strandedvector which includes within its sequence a DNA sequence encoding thedesired proteinaceous molecule. An oligonucleotide primer bearing thedesired mutated sequence is synthetically prepared. This primer is thenannealed with the single-stranded DNA preparation, and subjected to DNApolymerizing enzymes such as E. coli polymerase I Klenow fragment, inorder to complete the synthesis of the mutation-bearing strand. Thus, aheteroduplex is formed wherein one strand encodes the originalnon-mutated sequence and the second strand bears the desired mutation.This heteroduplex vector is then used to transform appropriate cells,such as E. coli cells, and clones are selected that include recombinantvectors bearing the mutated sequence arrangement.

The preparation of sequence variants of the selected gene usingsite-directed mutagenesis is provided as a means of producingpotentially useful species and is not meant to be limiting, as there areother ways in which sequence variants of genes may be obtained. Forexample, recombinant vectors encoding the desired gene may be treatedwith mutagenic agents, such as hydroxylamine, to obtain sequencevariants.

As modifications and changes may be made in the structure of the NGVNgenes, nucleic acids (e.g., nucleic acid segments) and proteinaceousmolecules of the present invention, and still obtain molecules havinglike or otherwise desirable characteristics, such biologicallyfunctional equivalents are also encompassed within the presentinvention.

For example, certain amino acids may be substituted for other aminoacids in a proteinaceous structure without appreciable loss ofinteractive binding capacity with structures such as, for example,antigen-binding regions of antibodies, binding sites on substratemolecules or receptors, or such like. Since it is the interactivecapacity and nature of a proteinaceous molecule that defines thatproteinaceous molecule's biological functional activity, certain aminoacid sequence substitutions can be made in a proteinaceous moleculesequence (or, of course, its underlying DNA coding sequence) andnevertheless obtain a proteinaceous molecule with like (agonistic)properties. It is thus contemplated that various changes may be made inthe sequence of NGVN proteins, polypeptides or peptides, or theunderlying nucleic acids, without appreciable loss of their biologicalutility or activity.

Equally, the same considerations may be employed to create a protein,polypeptide or peptide with countervailing, e.g., antagonisticproperties. This is relevant to the present invention in which NGVNmutants or analogues may be generated. For example, a NGVN mutant may begenerated and tested for NGVN activity to identify those residuesimportant for NGVN activity. NGVN mutants may also be synthesized toreflect a NGVN mutant that occurs in the human population and that islinked to the development of cancer. Such mutant proteinaceous moleculesare particularly contemplated for use in generating mutant-specificantibodies and such mutant DNA segments may be used as mutant-specificprobes and primers.

While discussion has focused on functionally equivalent polypeptidesarising from amino acid changes, it will be appreciated that thesechanges may be effected by alteration of the encoding DNA; taking intoconsideration also that the genetic code is degenerate and that two ormore codons may code for the same amino acid. A table of amino acids andtheir codons is presented herein above for use in such embodiments, aswell as for other uses, such as in the design of probes and primers andthe like.

In terms of functional equivalents, it is well understood by the skilledartisan that, inherent in the definition of a “biologically functionalequivalent” protein, polypeptide, peptide, gene or nucleic acid, is theconcept that there is a limit to the number of changes that may be madewithin a defined portion of the molecule and still result in a moleculewith an acceptable level of equivalent biological activity. Biologicallyfunctional equivalent peptides are thus defined herein as those peptidesin which certain, not most or all, of the amino acids may besubstituted.

In particular, where shorter length peptides are concerned, it iscontemplated that fewer amino acids changes should be made within thegiven peptide. Longer domains may have an intermediate number ofchanges. The full length protein will have the most tolerance for alarger number of changes. Of course, a plurality of distinctproteins/polypeptide/peptides with different substitutions may easily bemade and used in accordance with the invention.

It is also well understood that where certain residues are shown to beparticularly important to the biological or structural properties of aprotein, polypeptide or peptide, e.g., residues in binding regions oractive sites, such residues may not generally be exchanged. In thismanner, functional equivalents are defined herein as those peptideswhich maintain a substantial amount of their native biological activity.

Amino acid substitutions are generally based on the relative similarityof the amino acid side-chain substituents, for example, theirhydrophobicity, hydrophilicity, charge, size, and the like. An analysisof the size, shape and type of the amino acid side-chain substituentsreveals that arginine, lysine and histidine are all positively chargedresidues; that alanine, glycine and serine are all a similar size; andthat phenylalanine, tryptophan and tyrosine all have a generally similarshape. Therefore, based upon these considerations, arginine, lysine andhistidine; alanine, glycine and serine; and phenylalanine, tryptophanand tyrosine; are defined herein as biologically functional equivalents.

To effect more quantitative changes, the hydropathic index of aminoacids may be considered. Each amino acid has been assigned a hydropathicindex on the basis of their hydrophobicity and charge characteristics,these are: isoleucine (+4.5); valine (+4.2); leucine (+3.8);phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9);alanine (+1.8); glycine (−0.4); threonine (−0.7); serine (−0.8);tryptophan (−0.9); tyrosine (−1.3); proline (−1.6); histidine (−3.2);glutamate (−3.5); glutamine (−3.5); aspartate (−3.5); asparagine (−3.5);lysine (−3.9); and arginine (−4.5).

The importance of the hydropathic amino acid index in conferringinteractive biological function on a proteinaceous molecule is generallyunderstood in the art (Kyte & Doolittle, 1982, incorporated herein byreference). It is known that certain amino acids may be substituted forother amino acids having a similar hydropathic index or score and stillretain a similar biological activity. In making changes based upon thehydropathic index, the substitution of amino acids whose hydropathicindices are within ±2 is preferred, those which are within ±1 areparticularly preferred, and those within ±0.5 are even more particularlypreferred.

It is also understood in the art that the substitution of like aminoacids can be made effectively on the basis of hydrophilicity,particularly where the biological functional equivalent protein,polypeptide or peptide thereby created is intended for use inimmunological embodiments, as in certain embodiments of the presentinvention. U.S. Pat. No. 4,554,101, incorporated herein by reference,states that the greatest local average hydrophilicity of a proteinaceousmolecule, as governed by the hydrophilicity of its adjacent amino acids,correlates with its immunogenicity and antigenicity, i.e., with abiological property of the proteinaceous molecule.

As detailed in U.S. Pat. No. 4,554,101, the following hydrophilicityvalues have been assigned to amino acid residues: arginine (+3.0);lysine (+3.0); aspartate (+3.0±1); glutamate (+3.0±1); serine (+0.3);asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (−0.4);proline (−0.5±1); alanine (−0.5); histidine (−0.5); cysteine (−1.0);methionine (−1.3); valine (−1.5); leucine (−1.8); isoleucine (−1.8);tyrosine (−2.3); phenylalanine (−2.5); tryptophan (−3.4).

In making changes based upon similar hydrophilicity values, thesubstitution of amino acids whose hydrophilicity values are within ±2 ispreferred, those which are within ±1 are particularly preferred, andthose within ±0.5 are even more particularly preferred.

In addition to the NGVN peptidyl compounds described herein, it iscontemplated that other sterically similar compounds may be formulatedto mimic the key portions of the peptide structure. Such compounds,which may be termed peptidomimetics, may be used in the same manner asthe peptides of the invention and hence are also functional equivalents.

Certain mimetics that mimic elements of proteinaceous moleculessecondary structure are described in Johnson et al. (1993). Theunderlying rationale behind the use of peptide mimetics is that thepeptide backbone of proteinaceous molecules exists chiefly to orientateamino acid side chains in such a way as to facilitate molecularinteractions, such as those of antibody and antigen. A peptide mimeticis thus designed to permit molecular interactions similar to the naturalmolecule.

Some successful applications of the peptide mimetic concept have focusedon mimetics of β-turns within proteinaceous molecules, which are knownto be highly antigenic. Likely β-turn structure within a polypeptide canbe predicted by computer-based algorithms, as discussed herein. Once thecomponent amino acids of the turn are determined, mimetics can beconstructed to achieve a similar spatial orientation of the essentialelements of the amino acid side chains.

The generation of further structural equivalents or mimetics may beachieved by the techniques of modeling and chemical design known tothose of skill in the art. The art of receptor modeling is now wellknown, and by such methods a chemical that binds NGVN can be designedand then synthesized. It will be understood that all such stericallydesigned constructs fall within the scope of the present invention.

In addition to the 20 “standard” amino acids provided through thegenetic code, modified or unusual amino acids are also contemplated foruse in the present invention. A table of exemplary, but not limiting,modified or unusual amino acids is provided herein below.

TABLE 3 Modified and Unusual Amino Acids Abbr. Amino Acid Aad2-Aminoadipic acid Baad 3-Aminoadipic acid Bala Beta-alanine,beta-Amino-propionic acid Abu 2-Aminobutyric acid 4Abu 4-Aminobutyricacid, piperidinic acid Acp 6-Aminocaproic acid Ahe 2-Aminoheptanoic acidAib 2-Aminoisobutyric acid Baib 3-Aminoisobutyric acid Apm2-Aminopimelic acid Dbu 2,4-Diaminobutyric acid Des Desmosine Dpm2,2′-Diaminopimelic acid Dpr 2,3-Diaminopropionic acid EtGlyN-Ethylglycine EtAsn N-Ethylasparagine Hyl Hydroxylysine aHylAllo-Hydroxylysine 3Hyp 3-Hydroxyproline 4Hyp 4-Hydroxyproline IdeIsodesmosine aIle Allo-Isoleucine MeGly N-Methylglycine, sarcosine MeIleN-Methylisoleucine MeLys 6-N-Methyllysine MeVal N-Methylvaline NvaNorvaline Nle Norleucine Orn Ornithine

In one aspect, an compound may be designed by rational drug design tofunction as a NGVN in inhibition serine proteases. The goal of rationaldrug design is to produce structural analogs of biologically activecompounds. By creating such analogs, it is possible to fashion drugswhich are more active or stable than the natural molecules, which havedifferent susceptibility to alteration or which may affect the functionof various other molecules. In one approach, one would generate athree-dimensional structure for the NGVN protein of the invention or afragment thereof. This could be accomplished by X-ray crystallography,computer modeling or by a combination of both approaches. An alternativeapproach, involves the random replacement of functional groupsthroughout the NGVN protein, polypeptides or peptides, and the resultingaffect on function determined.

It also is possible to isolate a NGVN protein, polypeptide or peptidespecific antibody, selected by a functional assay, and then solve itscrystal structure. In principle, this approach yields a pharmacore uponwhich subsequent drug design can be based. It is possible to bypassprotein crystallography altogether by generating anti-idiotypicantibodies to a functional, pharmacologically active antibody. As amirror image of a mirror image, the binding site of anti-idiotype wouldbe expected to be an analog of the original antigen. The anti-idiotypecould then be used to identify and isolate peptides from banks ofchemically- or biologically-produced peptides. Selected peptides wouldthen serve as the pharmacore. Anti-idiotypes may be generated using themethods described herein for producing antibodies, using an antibody asthe antigen.

Thus, one may design drugs which have enhanced and improved biologicalactivity, for example, serine protease or tumor growth or metastasisinhibition, relative to a starting NGVN proteinaceous sequences. Byvirtue of the ability to recombinantly produce sufficient amounts of theNGVN proteins, polypeptides or peptides, crystallographic studies may bepreformed to determine the most likely sites for mutagenesis andchemical mimicry. In addition, knowledge of the chemical characteristicsof these compounds permits computer employed predictions ofstructure-function relationships. Computer models of various polypeptideand peptide structures are also available in the literature or computerdatabases. In a non-limiting example, the Entrez database(http://www.ncbi.nlm.nih.gov/Entrez/) may be used by one of ordinaryskill in the art to identify target sequences and regions formutagenesis.

3. Diagnosing BBS and Related Conditions

As discussed above, the present inventors have determined thatalterations in the NGVN gene are associated with BBS. Therefore, NGVNand the corresponding gene may be employed as a diagnostic or prognosticindicator of BBS in general, and of related disorders such as diabetes,hypertension, retinal degeneration, renal carcinoma, renal malformation,congenital heart defects, limb deformity and obesity. More specifically,point mutations, deletions, insertions or regulatory perturbationsrelating to NGVN will be identified. The present invention contemplatesfurther the diagnosis of disease states by detecting changes in thelevels of NGVN expression.

A. Genetic Diagnosis

One embodiment of the instant invention comprises a method for detectingvariation in the expression of NGVN. This may comprise determining thelevel of NGVN expressed, or determining specific alterations in theexpressed product. Obviously, this sort of assay has importance in thediagnosis of related BBS, but it also is relevant to other diseasestates such as diabetes, retinal degeneration, renal carcinoma(cancers), renal malformation, congenital heart defects, limb deformity,hypertension and obesity.

The biological sample can be any tissue or fluid. Various embodimentsinclude cells of the skin, muscle, fascia, brain, prostate, breast,endometrium, lung, head & neck, pancreas, small intestine, blood cells,liver, testes, ovaries, colon, rectum, skin, stomach, esophagus, spleen,lymph nodes, bone marrow or kidney. Other embodiments include fluidsamples such as peripheral blood, lymph fluid, ascites, serous fluid,pleural effusion, sputum, cerebrospinal fluid, lacrimal fluid, stoolurine or amniotic fluid.

Nucleic acids used are isolated from cells contained in the biologicalsample, according to standard methodologies (Sambrook et al., 1989). Thenucleic acid may be genomic DNA or fractionated or whole cell RNA. WhereRNA is used, it may be desired to convert the RNA to a complementary DNA(cDNA). In one embodiment, the RNA is whole cell RNA; in another, it ispoly-A RNA. Normally, the nucleic acid is amplified.

Depending on the format, the specific nucleic acid of interest isidentified in the sample directly using amplification or with a second,known nucleic acid following amplification. Next, the identified productis detected. In certain applications, the detection may be performed byvisual means (e.g., ethidium bromide staining of a gel). Alternatively,the detection may involve indirect identification of the product viachemiluminescence, radioactive scintigraphy of radiolabel or fluorescentlabel or even via a system using electrical or thermal impulse signals(Affymax Technology; Bellus, 1994).

Following detection, one may compare the results seen in a given patientwith a statistically significant reference group of normal patients andpatients that have BBS or BBS-related pathologies. In this way, it ispossible to correlate the amount or kind of BBS detected with variousclinical states.

Various types of defects have been identified by the present inventors.Thus, “alterations” should be read as including deletions, insertions,point mutations and duplications. Point mutations result in stop codons,frameshift mutations or amino acid substitutions. Somatic mutations arethose occurring in non-germline tissues. Germ-line tissue can occur inany tissue and are inherited. Mutations in and outside the coding regionalso may affect the amount of NGVN produced, both by altering thetranscription of the gene or in destabilizing or otherwise altering theprocessing of either the transcript (mRNA) or protein.

The following table provides a summary of the changes identified in theNGVN gene:

TABLE 4 Exon # DNA Change (cDNA base) Protein Change 02 T224G Val75Gly08 C814T Arg272Stop 08 C823T Arg275Stop 08 940delA Frameshift 101206insA Frameshift 03 A367G Ile123Val 12 A1413C Val471Val

It is contemplated that other mutations in the NGVN gene may beidentified in accordance with the present invention by detecting anucleotide change in particular nucleic acids (U.S. Pat. No. 4,988,617,incorporated herein by reference). A variety of different assays arecontemplated in this regard, including but not limited to, fluorescentin situ hybridization (FISH; U.S. Pat. No. 5,633,365 and U.S. Pat. No.5,665,549, each incorporated herein by reference), direct DNAsequencing, PFGE analysis, Southern or Northern blotting,single-stranded conformation analysis (SSCA), RNAse protection assay,allele-specific oligonucleotide (ASO, e.g., U.S. Pat. No. 5,639,611),dot blot analysis, denaturing gradient gel electrophoresis (e.g., U.S.Pat. No. 5,190,856 incorporated herein by reference), RFLP (e.g., U.S.Pat. No. 5,324,631 incorporated herein by reference) and PCR™-SSCP.Methods for detecting and quantitating gene sequences, such as mutatedgenes and oncogenes, in for example biological fluids are described inU.S. Pat. No. 5,496,699, incorporated herein by reference.

a. Primers and Probes

The term primer, as defined herein, is meant to encompass any nucleicacid that is capable of priming the synthesis of a nascent nucleic acidin a template-dependent process. Typically, primers are oligonucleotidesfrom ten to twenty base pairs in length, but longer sequences can beemployed. Primers may be provided in double-stranded or single-strandedform, although the single-stranded form is preferred. Probes are defineddifferently, although they may act as primers. Probes, while perhapscapable of priming, are designed to binding to the target DNA or RNA andneed not be used in an amplification process.

In preferred embodiments, the probes or primers are labeled withradioactive species (³²P, ¹⁴C, ³⁵S, ³H, or other label), with afluorophore (rhodamine, fluorescein) or a chemillumiscent (luciferase).

b. Template Dependent Amplification Methods

A number of template dependent processes are available to amplify themarker sequences present in a given template sample. One of the bestknown amplification methods is the polymerase chain reaction (referredto as PCR™) which is described in detail in U.S. Pat. Nos. 4,683,195,4,683,202 and 4,800,159, and in Innis et al., 1990, each of which isincorporated herein by reference in its entirety.

Briefly, in PCR™, two primer sequences are prepared that arecomplementary to regions on opposite complementary strands of the markersequence. An excess of deoxynucleoside triphosphates are added to areaction mixture along with a DNA polymerase, e.g., Taq polymerase. Ifthe marker sequence is present in a sample, the primers will bind to themarker and the polymerase will cause the primers to be extended alongthe marker sequence by adding on nucleotides. By raising and loweringthe temperature of the reaction mixture, the extended primers willdissociate from the marker to form reaction products, excess primerswill bind to the marker and to the reaction products and the process isrepeated.

A reverse transcriptase PCR™ amplification procedure may be performed inorder to quantify the amount of mRNA amplified. Methods of reversetranscribing RNA into cDNA are well known and described in Sambrook etal., 1989. Alternative methods for reverse transcription utilizethermostable, RNA-dependent DNA polymerases. These methods are describedin WO 90/07641 filed Dec. 21, 1990, Polymerase chain reactionmethodologies are well known in the art.

Another method for amplification is the ligase chain reaction (“LCR”U.S. Pat. Nos. 5,494,810, 5,484,699, EP 320 308, each incorporatedherein by reference). In LCR, two complementary probe pairs areprepared, and in the presence of the target sequence, each pair willbind to opposite complementary strands of the target such that theyabout. In the presence of a ligase, the two probe pairs will link toform a single unit. By temperature cycling, as in PCR™, bound ligatedunits dissociate from the target and then serve as “target sequences”for ligation of excess probe pairs. U.S. Pat. No. 4,883,750 describes amethod similar to LCR for binding probe pairs to a target sequence.

Qbeta Replicase an RNA-directed RNA polymerase, also may be used asstill another amplification method in the present invention. In thismethod, a replicative sequence of RNA that has a region complementary tothat of a target is added to a sample in the presence of an RNApolymerase. The polymerase will copy the replicative sequence that canthen be detected. Similar methods also are described in U.S. Pat. No.4,786,600, incorporated herein by reference, which concerns recombinantRNA molecules capable of serving as a template for the synthesis ofcomplementary single-stranded molecules by RNA-directed RNA polymerase.The product molecules so formed also are capable of serving as atemplate for the synthesis of additional copies of the originalrecombinant RNA molecule.

An isothermal amplification method, in which restriction endonucleasesand ligases are used to achieve the amplification of target moleculesthat contain nucleotide 5′-[alpha-thio]-triphosphates in one strand of arestriction site also may be useful in the amplification of nucleicacids in the present invention (Walker et al., 1992; U.S. Pat. No.5,270,184, incorporated herein by reference). U.S. Pat. No. 5,747,255(incorporated herein by reference) describes an isothermal amplificationusing cleavable oligonucleotides for polynucleotide detection. In themethod described therein, separated populations of oligonucleotides areprovided that contain complementary sequences to one another and thatcontain at least one scissile linkage which is cleaved whenever aperfectly matched duplex is formed containing the linkage. When a targetpolynucleotide contacts a first oligonucleotide cleavage occurs and afirst fragment is produced which can hybridize with a secondoligonucleotide. Upon such hybridization, the second oligonucleotide iscleaved releasing a second fragment that can, in turn, hybridize with afirst oligonucleotide in a manner similar to that of the targetpolynucleotide.

Strand Displacement Amplification (SDA) is another method of carryingout isothermal amplification of nucleic acids which involves multiplerounds of strand displacement and synthesis, i.e., nick translation(e.g., U.S. Pat. Nos. 5,744,311; 5,733,752; 5,733,733; 5,712,124). Asimilar method, called Repair Chain Reaction (RCR), involves annealingseveral probes throughout a region targeted for amplification, followedby a repair reaction in which only two of the four bases are present.The other two bases can be added as biotinylated derivatives for easydetection. A similar approach is used in SDA. Target specific sequencescan also be detected using a cyclic probe reaction (CPR). In CPR, aprobe having 3′ and 5′ sequences of non-specific DNA and a middlesequence of specific RNA is hybridized to DNA that is present in asample. Upon hybridization, the reaction is treated with RNase H, andthe products of the probe identified as distinctive products that arereleased after digestion. The original template is annealed to anothercycling probe and the reaction is repeated.

Still another amplification methods described in GB Application No. 2202 328, and in PCT Application No. PCT/US89/01025, each of which isincorporated herein by reference in its entirety, may be used inaccordance with the present invention. In the former application,“modified” primers are used in a PCR™-like, template- andenzyme-dependent synthesis. The primers may be modified by labeling witha capture moiety (e.g., biotin) and/or a detector moiety (e.g., enzyme).In the latter application, an excess of labeled probes are added to asample. In the presence of the target sequence, the probe binds and iscleaved catalytically. After cleavage, the target sequence is releasedintact to be bound by excess probe. Cleavage of the labeled probesignals the presence of the target sequence.

Other nucleic acid amplification procedures include transcription-basedamplification systems (TAS), including nucleic acid sequence basedamplification (NASBA) and 3SR (Kwoh et al., 1989; Gingeras et al., PCTApplication WO 88/10315, incorporated herein by reference in theirentirety). In NASBA, the nucleic acids can be prepared for amplificationby standard phenol/chloroform extraction, heat denaturation of aclinical sample, treatment with lysis buffer and minispin columns forisolation of DNA and RNA or guanidinium chloride extraction of RNA.These amplification techniques involve annealing a primer which hastarget specific sequences. Following polymerization, DNA/RNA hybrids aredigested with RNase H while double stranded DNA molecules are heatdenatured again. In either case the single stranded DNA is made fullydouble stranded by addition of second target specific primer, followedby polymerization. The double-stranded DNA molecules are then multiplytranscribed by an RNA polymerase such as T7 or SP6. In an isothermalcyclic reaction, the RNA's are reverse transcribed into single strandedDNA, which is then converted to double stranded DNA, and thentranscribed once again with an RNA polymerase such as T7 or SP6. Theresulting products, whether truncated or complete, indicate targetspecific sequences.

Davey et al., EP 329 822 (incorporated herein by reference in itsentirety) disclose a nucleic acid amplification process involvingcyclically synthesizing single-stranded RNA (“ssRNA”), ssDNA, anddouble-stranded DNA (dsDNA), which may be used in accordance with thepresent invention. The ssRNA is a template for a first primeroligonucleotide, which is elongated by reverse transcriptase(RNA-dependent DNA polymerase). The RNA is then removed from theresulting DNA:RNA duplex by the action of ribonuclease H(RNase H, anRNase specific for RNA in duplex with either DNA or RNA). The resultantssDNA is a template for a second primer, which also includes thesequences of an RNA polymerase promoter (exemplified by T7 RNApolymerase) 5′ to its homology to the template. This primer is thenextended by DNA polymerase (exemplified by the large “Klenow” fragmentof E. coli DNA polymerase I), resulting in a double-stranded DNA(“dsDNA”) molecule, having a sequence identical to that of the originalRNA between the primers and having additionally, at one end, a promotersequence. This promoter sequence can be used by the appropriate RNApolymerase to make many RNA copies of the DNA. These copies can thenre-enter the cycle leading to very swift amplification. With properchoice of enzymes, this amplification can be done isothermally withoutaddition of enzymes at each cycle. Because of the cyclical nature ofthis process, the starting sequence can be chosen to be in the form ofeither DNA or RNA.

Miller et al., PCT Application WO 89/06700 (incorporated herein byreference in its entirety) disclose a nucleic acid sequenceamplification scheme based on the hybridization of a promoter/primersequence to a target single-stranded DNA (“ssDNA”) followed bytranscription of many RNA copies of the sequence. This scheme is notcyclic, i.e., new templates are not produced from the resultant RNAtranscripts. Other amplification methods include “RACE” and “one-sidedPCR™” (Frohman, 1990; Ohara et al., 1989; each herein incorporated byreference in their entirety).

Methods based on ligation of two (or more) oligonucleotides in thepresence of nucleic acid having the sequence of the resulting“di-oligonucleotide”, thereby amplifying the di-oligonucleotide, alsomay be used in the amplification step of the present invention. Wu etal., (1989), incorporated herein by reference in its entirety.

c. Southern/Northern Blotting

Blotting techniques are well known to those of skill in the art.Southern blotting involves the use of DNA as a target, whereas Northernblotting involves the use of RNA as a target. Each provide differenttypes of information, although cDNA blotting is analogous, in manyaspects, to blotting or RNA species.

Briefly, a probe is used to target a DNA or RNA species that has beenimmobilized on a suitable matrix, often a filter of nitrocellulose. Thedifferent species should be spatially separated to facilitate analysis.This often is accomplished by gel electrophoresis of nucleic acidspecies followed by “blotting” on to the filter.

Subsequently, the blotted target is incubated with a probe (usuallylabeled) under conditions that promote denaturation and rehybridization.Because the probe is designed to base pair with the target, the probewill binding a portion of the target sequence under renaturingconditions. Unbound probe is then removed, and detection is accomplishedas described above.

d. Separation Methods

It normally is desirable, at one stage or another, to separate theamplification product from the template and the excess primer for thepurpose of determining whether specific amplification has occurred. Inone embodiment, amplification products are separated by agarose,agarose-acrylamide or polyacrylamide gel electrophoresis using standardmethods (See Sambrook et al., 1989).

Alternatively, chromatographic techniques may be employed to effectseparation. There are many kinds of chromatography which may be used inthe present invention: adsorption, partition, ion-exchange and molecularsieve, and many specialized techniques for using them including column,paper, thin-layer and gas chromatography (Freifelder, 1982).

e. Detection Methods

Products may be visualized in order to confirm amplification of themarker sequences. One typical visualization method involves staining ofa gel with ethidium bromide and visualization under UV light.Alternatively, if the amplification products are integrally labeled withradio- or fluorometrically-labeled nucleotides, the amplificationproducts can then be exposed to x-ray film or visualized under theappropriate stimulating spectra, following separation.

In one embodiment, visualization is achieved indirectly. Followingseparation of amplification products, a labeled nucleic acid probe isbrought into contact with the amplified marker sequence. The probepreferably is conjugated to a chromophore but may be radiolabeled. Inanother embodiment, the probe is conjugated to a binding partner, suchas an antibody or biotin, and the other member of the binding paircarries a detectable moiety.

In one embodiment, detection is by a labeled probe. The techniquesinvolved are well known to those of skill in the art and can be found inmany standard books on molecular protocols. See Sambrook et al., 1989.For example, chromophore or radiolabel probes or primers identify thetarget during or following amplification.

One example of the foregoing is described in U.S. Pat. No. 5,279,721,incorporated by reference herein, which discloses an apparatus andmethod for the automated electrophoresis and transfer of nucleic acids.The apparatus permits electrophoresis and blotting without externalmanipulation of the gel and is ideally suited to carrying out methodsaccording to the present invention.

In addition, the amplification products described above may be subjectedto sequence analysis to identify specific kinds of variations usingstandard sequence analysis techniques. Within certain methods,exhaustive analysis of genes is carried out by sequence analysis usingprimer sets designed for optimal sequencing (Pignon et al., 1994). Thepresent invention provides methods by which any or all of these types ofanalyses may be used. Using the sequences disclosed herein,oligonucleotide primers may be designed to permit the amplification ofsequences throughout the NGVN gene that may then be analyzed by directsequencing.

f. Kit Components

All the essential materials and reagents required for detecting andsequencing NGVN and variants thereof may be assembled together in a kit.This generally will comprise preselected primers and probes. Alsoincluded may be enzymes suitable for amplifying nucleic acids includingvarious polymerases (RT, Taq, Sequenase™, etc.), deoxynucleotides andbuffers to provide the necessary reaction mixture for amplification.Such kits also generally will comprise, in suitable means, distinctcontainers for each individual reagent and enzyme as well as for eachprimer or probe.

g. Design and Theoretical Considerations for Relative QuantitativeRT-PCR™

Reverse transcription (RT) of RNA to cDNA followed by relativequantitative PCR™ (RT-PCR™) can be used to determine the relativeconcentrations of specific mRNA species isolated from patients. Bydetermining that the concentration of a specific mRNA species varies, itis shown that the gene encoding the specific mRNA species isdifferentially expressed.

In PCR™, the number of molecules of the amplified target DNA increase bya factor approaching two with every cycle of the reaction until somereagent becomes limiting. Thereafter, the rate of amplification becomesincreasingly diminished until there is no increase in the amplifiedtarget between cycles. If a graph is plotted in which the cycle numberis on the X axis and the log of the concentration of the amplifiedtarget DNA is on the Y axis, a curved line of characteristic shape isformed by connecting the plotted points. Beginning with the first cycle,the slope of the line is positive and constant. This is said to be thelinear portion of the curve. After a reagent becomes limiting, the slopeof the line begins to decrease and eventually becomes zero. At thispoint the concentration of the amplified target DNA becomes asymptoticto some fixed value. This is said to be the plateau portion of thecurve.

The concentration of the target DNA in the linear portion of the PCR™amplification is directly proportional to the starting concentration ofthe target before the reaction began. By determining the concentrationof the amplified products of the target DNA in PCR™ reactions that havecompleted the same number of cycles and are in their linear ranges, itis possible to determine the relative concentrations of the specifictarget sequence in the original DNA mixture. If the DNA mixtures arecDNAs synthesized from RNAs isolated from different tissues or cells,the relative abundances of the specific mRNA from which the targetsequence was derived can be determined for the respective tissues orcells. This direct proportionality between the concentration of the PCR™products and the relative mRNA abundances is only true in the linearrange of the PCR™ reaction.

The final concentration of the target DNA in the plateau portion of thecurve is determined by the availability of reagents in the reaction mixand is independent of the original concentration of target DNA.Therefore, the first condition that must be met before the relativeabundances of a mRNA species can be determined by RT-PCR™ for acollection of RNA populations is that the concentrations of theamplified PCR™ products must be sampled when the PCR™ reactions are inthe linear portion of their curves.

The second condition that must be met for an RT-PCR™ experiment tosuccessfully determine the relative abundances of a particular mRNAspecies is that relative concentrations of the amplifiable cDNAs must benormalized to some independent standard. The goal of an RT-PCR™experiment is to determine the abundance of a particular mRNA speciesrelative to the average abundance of all mRNA species in the sample. Inthe experiments described below, mRNAs for β-actin, asparaginesynthetase and lipocortin II were used as external and internalstandards to which the relative abundance of other mRNAs are compared.

Most protocols for competitive PCR™ utilize internal PCR™ standards thatare approximately as abundant as the target. These strategies areeffective if the products of the PCR™ amplifications are sampled duringtheir linear phases. If the products are sampled when the reactions areapproaching the plateau phase, then the less abundant product becomesrelatively over represented. Comparisons of relative abundances made formany different RNA samples, such as is the case when examining RNAsamples for differential expression, become distorted in such a way asto make differences in relative abundances of RNAs appear less than theyactually are. This is not a significant problem if the internal standardis much more abundant than the target. If the internal standard is moreabundant than the target, then direct linear comparisons can be madebetween RNA samples.

The above discussion describes theoretical considerations for an RT-PCR™assay for clinically derived materials. The problems inherent inclinical samples are that they are of variable quantity (makingnormalization problematic), and that they are of variable quality(necessitating the co-amplification of a reliable internal control,preferably of larger size than the target). Both of these problems areovercome if the RT-PCR™ is performed as a relative quantitative RT-PCR™with an internal standard in which the internal standard is anamplifiable cDNA fragment that is larger than the target cDNA fragmentand in which the abundance of the mRNA encoding the internal standard isroughly 5-100 fold higher than the mRNA encoding the target. This assaymeasures relative abundance, not absolute abundance of the respectivemRNA species.

Other studies may be performed using a more conventional relativequantitative RT-PCR™ assay with an external standard protocol. Theseassays sample the PCR™ products in the linear portion of theiramplification curves. The number of PCR™ cycles that are optimal forsampling must be empirically determined for each target cDNA fragment.In addition, the reverse transcriptase products of each RNA populationisolated from the various tissue samples must be carefully normalizedfor equal concentrations of amplifiable cDNAs. This consideration isvery important since the assay measures absolute mRNA abundance.Absolute mRNA abundance can be used as a measure of differential geneexpression only in normalized samples. While empirical determination ofthe linear range of the amplification curve and normalization of cDNApreparations are tedious and time consuming processes, the resultingRT-PCR™ assays can be superior to those derived from the relativequantitative RT-PCR™ assay with an internal standard.

One reason for this advantage is that without the internalstandard/competitor, all of the reagents can be converted into a singlePCR™ product in the linear range of the amplification curve, thusincreasing the sensitivity of the assay. Another reason is that withonly one PCR™ product, display of the product on an electrophoretic gelor another display method becomes less complex, has less background andis easier to interpret.

h. Chip Technologies

Specifically contemplated by the present inventors are chip-based DNAtechnologies such as those described by Hacia et al. (1996) andShoemaker et al. (1996). Briefly, these techniques involve quantitativemethods for analyzing large numbers of genes rapidly and accurately. Bytagging genes with oligonucleotides or using fixed probe arrays, one canemploy chip technology to segregate target molecules as high densityarrays and screen these molecules on the basis of hybridization. Seealso Pease et al., (1994); Fodor et al., (1991).

B. Immunodiagnosis

Antibodies can be used in characterizing the NGVN content of healthy anddiseased tissues, through techniques such as ELISAs and Westernblotting. This may provide a prenatal screen or in counseling for thoseindividuals seeking to have children.

The use of antibodies of the present invention, in an ELISA assay iscontemplated. For example, anti-NGVN antibodies are immobilized onto aselected surface, preferably a surface exhibiting a protein affinitysuch as the wells of a polystyrene microtiter plate. After washing toremove incompletely adsorbed material, it is desirable to bind or coatthe assay plate wells with a non-specific protein that is known to beantigenically neutral with regard to the test antisera such as bovineserum albumin (BSA), casein or solutions of powdered milk. This allowsfor blocking of non-specific adsorption sites on the immobilizingsurface and thus reduces the background caused by non-specific bindingof antigen onto the surface.

After binding of antibody to the well, coating with a non-reactivematerial to reduce background, and washing to remove unbound material,the immobilizing surface is contacted with the sample to be tested in amanner conducive to immune complex (antigen/antibody) formation.

Following formation of specific immunocomplexes between the test sampleand the bound antibody, and subsequent washing, the occurrence and evenamount of immunocomplex formation may be determined by subjecting sameto a second antibody having specificity for NGVN that differs the firstantibody. Appropriate conditions preferably include diluting the samplewith diluents such as BSA, bovine gamma globulin (BGG) and phosphatebuffered saline (PBS)/Tween®. These added agents also tend to assist inthe reduction of nonspecific background. The layered antisera is thenallowed to incubate for from about 2 to about 4 hr, at temperaturespreferably on the order of about 25° to about 27° C. Followingincubation, the antisera-contacted surface is washed so as to removenon-immunocomplexed material. A preferred washing procedure includeswashing with a solution such as PBS/Tween®, or borate buffer.

To provide a detecting means, the second antibody will preferably havean associated enzyme that will generate a color development uponincubating with an appropriate chromogenic substrate. Thus, for example,one will desire to contact and incubate the second antibody-boundsurface with a urease or peroxidase-conjugated anti-human IgG for aperiod of time and under conditions which favor the development ofimmunocomplex formation (e.g., incubation for 2 hr at room temperaturein a PBS-containing solution such as PBS/Tween®).

After incubation with the second enzyme-tagged antibody, and subsequentto washing to remove unbound material, the amount of label is quantifiedby incubation with a chromogenic substrate such as urea and bromocresolpurple or 2,2′-azino-di-(3-ethyl-benzthiazoline)-6-sulfonic acid (ABTS)and H₂O₂, in the case of peroxidase as the enzyme label. Quantitation isthen achieved by measuring the degree of color generation, e.g., using avisible spectrum spectrophotometer.

The preceding format may be altered by first binding the sample to theassay plate. Then, primary antibody is incubated with the assay plate,followed by detecting of bound primary antibody using a labeled secondantibody with specificity for the primary antibody.

The steps of various other useful immunodetection methods have beendescribed in the scientific literature, such as, e.g., Nakamura et al.,(1987). Immunoassays, in their most simple and direct sense, are bindingassays. Certain preferred immunoassays are the various types ofradioimmunoassays (RIA) and immunobead capture assay.Immunohistochemical detection using tissue sections also is particularlyuseful. However, it will be readily appreciated that detection is notlimited to such techniques, and Western blotting, dot blotting, FACSanalyses, and the like also may be used in connection with the presentinvention.

The antibody compositions of the present invention will find great usein immunoblot or Western blot analysis. The antibodies may be used ashigh-affinity primary reagents for the identification of proteinsimmobilized onto a solid support matrix, such as nitrocellulose, nylonor combinations thereof. In conjunction with immunoprecipitation,followed by gel electrophoresis, these may be used as a single stepreagent for use in detecting antigens against which secondary reagentsused in the detection of the antigen cause an adverse background.Immunologically-based detection methods for use in conjunction withWestern blotting include enzymatically-, radiolabel-, orfluorescently-tagged secondary antibodies against the toxin moiety areconsidered to be of particular use in this regard. U.S. patentsconcerning the use of such labels include U.S. Pat. Nos. 3,817,837;3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149 and 4,366,241,each incorporated herein by reference. Of course, one may findadditional advantages through the use of a secondary binding ligand suchas a second antibody or a biotin/avidin ligand binding arrangement, asis known in the art.

4. Methods for Screening Active Compounds

The present invention also contemplates the use of NGVN and activefragments, and nucleic acids coding therefor, in the screening ofcompounds for activity in either stimulating NGVN activity, overcomingthe lack of NGVN or blocking the effect of a mutant NGVN molecule. Theseassays may make use of a variety of different formats and may depend onthe kind of “activity” for which the screen is being conducted.

A. In Vitro Assays

In one embodiment, the invention is to be applied for the screening ofcompounds that bind to the NGVN polypeptide or fragment thereof. Thepolypeptide or fragment may be either free in solution, fixed to asupport, expressed in or on the surface of a cell. Either thepolypeptide or the compound may be labeled, thereby permittingdetermining of binding.

In another embodiment, the assay may measure the inhibition of bindingof NGVN to a natural or artificial substrate or binding partner.Competitive binding assays can be performed in which one of the agents(NGVN, binding partner or compound) is labeled. Usually, the polypeptidewill be the labeled species. One may measure the amount of free labelversus bound label to determine binding or inhibition of binding.

Another technique for high throughput screening of compounds isdescribed in WO 84/03564. Large numbers of small peptide test compoundsare synthesized on a solid substrate, such as plastic pins or some othersurface. The peptide test compounds are reacted with NGVN and washed.Bound polypeptide is detected by various methods.

Purified NGVN can be coated directly onto plates for use in theaforementioned drug screening techniques. However, non-neutralizingantibodies to the polypeptide can be used to immobilize the polypeptideto a solid phase. Also, fusion proteins containing a reactive region(preferably a terminal region) may be used to link the NGVN activeregion to a solid phase.

Various cell lines containing wild-type or natural or engineeredmutations in NGVN gene can be used to study various functionalattributes of NGVN and how a candidate compound affects theseattributes. Methods for engineering mutations are described elsewhere inthis document, as are naturally-occurring mutations in NGVN that leadto, contribute to and/or otherwise cause BBS. In such assays, thecompound would be formulated appropriately, given its biochemicalnature, and contacted with a target cell. Depending on the assay,culture may be required. The cell may then be examined by virtue of anumber of different physiologic assays. Alternatively, molecularanalysis may be performed in which the function of NGVN, or relatedpathways, may be explored.

B. In Vivo Assays

The present invention also encompasses the use of various animal models.Thus, any identity seen between human and other animal NGVN provides anexcellent opportunity to examine the function of NGVN in a whole animalsystem where it is normally expressed. By developing or isolating mutantcells lines that fail to express normal NGVN, one can generate models inmice that will be highly predictive of BBS and related syndromes inhumans and other mammals.

Treatment of animals with test compounds will involve the administrationof the compound, in an appropriate form, to the animal. Administrationwill be by any route the could be utilized for clinical or non-clinicalpurposes, including but not limited to oral, nasal, buccal, rectal,vaginal or topical. Alternatively, administration may be byintratracheal instillation, bronchial instillation, intradermal,subcutaneous, intramuscular, intraperitoneal or intravenous injection.Specifically contemplated are systemic intravenous injection, regionaladministration via blood or lymph supply and intratumoral injection.

Determining the effectiveness of a compound in vivo may involve avariety of different criteria. Such criteria include, but are notlimited to, survival, reduction of tumor burden or mass, arrest orslowing of tumor progression, elimination of tumors, inhibition orprevention of metastasis, increased activity level, improvement inimmune effector function and improved food intake.

C. Rational Drug Design

The goal of rational drug design is to produce structural analogs ofbiologically active polypeptides or compounds with which they interact(agonists, antagonists, inhibitors, binding partners, etc.). By creatingsuch analogs, it is possible to fashion drugs which are more active orstable than the natural molecules, which have different susceptibilityto alteration or which may affect the function of various othermolecules. In one approach, one would generate a three-dimensionalstructure for NGVN or a fragment thereof. This could be accomplished byx-ray crystallography, computer modeling or by a combination of bothapproaches. An alternative approach, “alanine scan,” involves the randomreplacement of residues throughout molecule with alanine, and theresulting affect on function determined.

It also is possible to isolate a NGVN-specific antibody, selected by afunctional assay, and then solve its crystal structure. In principle,this approach yields a pharmacore upon which subsequent drug design canbe based. It is possible to bypass protein crystallograph altogether bygenerating anti-idiotypic antibodies to a functional, pharmacologicallyactive antibody. As a mirror image of a mirror image, the binding siteof anti-idiotype would be expected to be an analog of the originalantigen. The anti-idiotype could then be used to identify and isolatepeptides from banks of chemically- or biologically-produced peptides.Selected peptides would then serve as the pharmacore. Anti-idiotypes maybe generated using the methods described herein for producingantibodies, using an antibody as the antigen.

Thus, one may design drugs which have improved NGVN activity or whichact as stimulators, inhibitors, agonists, antagonists of NGVN ormolecules affected by NGVN function. By virtue of the availability ofcloned NGVN gene sequences, sufficient amounts of NGVN can be producedto perform crystallographic studies. In addition, knowledge of thepolypeptide sequences permits computer employed predictions ofstructure-function relationships.

D. Transgenic Animals/Knockout Animals

In one embodiment of the invention, transgenic animals are producedwhich contain a functional transgene encoding a functional NGVNpolypeptide or variants thereof. Transgenic animals expressing NGVNtransgenes, recombinant cell lines derived from such animals andtransgenic embryos may be useful in methods for screening for andidentifying agents that induce or repress function of NGVN. Transgenicanimals of the present invention also can be used as models for studyingdisease states.

In one embodiment of the invention, a NGVN transgene is introduced intoa non-human host to produce a transgenic animal expressing a human ormurine NGVN gene. The transgenic animal is produced by the integrationof the transgene into the genome in a manner that permits the expressionof the transgene. Methods for producing transgenic animals are generallydescribed by Wagner and Hoppe (U.S. Pat. No. 4,873,191; which isincorporated herein by reference), Brinster et al., 1985; which isincorporated herein by reference in its entirety) and in “Manipulatingthe Mouse Embryo; A Laboratory Manual” 2nd edition (eds., Hogan,Beddington, Costantimi and Long, Cold Spring Harbor Laboratory Press,1994; which is incorporated herein by reference in its entirety).

It may be desirable to replace the endogenous NGVN by homologousrecombination between the transgene and the endogenous gene; or theendogenous gene may be eliminated by deletion as in the preparation of“knock-out” animals. Typically, a NGVN gene flanked by genomic sequencesis transferred by microinjection into a fertilized egg. Themicroinjected eggs are implanted into a host female, and the progeny arescreened for the expression of the transgene. Transgenic animals may beproduced from the fertilized eggs from a number of animals including,but not limited to reptiles, amphibians, birds, mammals, and fish.Within a particularly preferred embodiment, transgenic mice aregenerated which overexpress NGVN or express a mutant form of thepolypeptide. Alternatively, the absence of a NGVN in “knock-out” micepermits the study of the effects that loss of NGVN protein has on a cellin vivo. Knock-out mice also provide a model for the development ofNGVN-related disease.

As noted above, transgenic animals and cell lines derived from suchanimals may find use in certain testing experiments. In this regard,transgenic animals and cell lines capable of expressing wild-type ormutant NGVN may be exposed to test substances. These test substances canbe screened for the ability to enhance wild-type NGVN expression and orfunction or impair the expression or function of mutant NGVN.

5. Methods for Treating BBS

The present invention also contemplates the treatment of BBS and relatedsymptoms such as obesity, diabetes, renal cancer or other abnormalities,retinal degeneration and hypertension by providing a NGVN protein tocells of an affected individual.

A. Genetic Based Therapies

Specifically, the present inventors intend to provide, to a cell, anexpression construct capable of providing NGVN to that cell. Because thesequence homology between the human, and other NGVN, any of thesenucleic acids could be used in human therapy, as could any of the genesequence variants discussed above which would encode the same, or abiologically equivalent polypeptide. The lengthy discussion ofexpression vectors and the genetic elements employed therein isincorporated into this section by reference. Particularly preferredexpression vectors are viral vectors such as adenovirus,adeno-associated virus, herpesvirus; vaccinia virus and retrovirus. Alsopreferred is liposomally-encapsulated expression vector.

Those of skill in the art are well aware of how to apply gene deliveryto in vivo and ex vivo situations. For viral vectors, one generally willprepare a viral vector stock. Depending on the kind of virus and thetiter attainable, one will deliver 1×10⁴, 1×10⁵, 1×10⁶, 1×10⁷, 1×10⁸,1×10⁹, 1×10¹⁰, 1×10¹¹ or 1×10¹² infectious particles to the patient.Similar figures may be extrapolated for liposomal or other non-viralformulations by comparing relative uptake efficiencies. Formulation as apharmaceutically acceptable composition is discussed below.

B. Protein Therapy

Another therapy approach is the provision, to a subject, of NGVNpolypeptide, active fragments, synthetic peptides, mimetics or otheranalogs thereof. The protein may be produced by recombinant expressionmeans. Formulations would be selected based on the route ofadministration and purpose including, but not limited to, liposomalformulations and classic pharmaceutical preparations.

6. Engineering Expression Constructs

In certain embodiments, the present invention involves the manipulationof genetic material to produce expression constructs that encode NGVNgene. Such methods involve the generation of expression constructscontaining, for example, a heterologous DNA encoding a gene of interestand a means for its expression, replicating the vector in an appropriatehelper cell, obtaining viral particles produced therefrom, and infectingcells with the recombinant virus particles.

The gene will be a normal NGVN gene discussed herein above. In thecontext of gene therapy, the gene will be a heterologous DNA, meant toinclude DNA derived from a source other than the viral genome whichprovides the backbone of the vector. The gene may be derived from aprokaryotic or eukaryotic source such as a bacterium, a virus, a yeast,a parasite, a plant, or even an animal. The heterologous DNA also may bederived from more than one source, i.e., a multigene construct or afusion protein. The heterologous DNA also may include a regulatorysequence which may be derived from one source and the gene from adifferent source.

A. Selectable Markers

In certain embodiments of the invention, the therapeutic expressionconstructs of the present invention contain nucleic acid constructswhose expression may be identified in vitro or in vivo by including amarker in the expression construct. Such markers would confer anidentifiable change to the cell permitting easy identification of cellscontaining the expression construct. Usually the inclusion of a drugselection marker aids in cloning and in the selection of transformants.For example, genes that confer resistance to neomycin, puromycin,hygromycin, DHFR, GPT, zeocin and histidinol are useful selectablemarkers. Alternatively, enzymes such as herpes simplex virus thymidinekinase (tk) may be employed. Immunologic markers also can be employed.The selectable marker employed is not believed to be important, so longas it is capable of being expressed simultaneously with the nucleic acidencoding a gene product. Further examples of selectable markers are wellknown to one of skill in the art and include reporters such as EGFP,β-gal or chloramphenicol acetyltransferase (CAT).

B. Control Regions

a. Promoters

Throughout this application, the term “expression construct” is meant toinclude any type of genetic construct containing a nucleic acid codingfor gene products in which part or all of the nucleic acid encodingsequence is capable of being transcribed. The transcript may betranslated into a protein, but it need not be. In certain embodiments,expression includes both transcription of a gene and translation of mRNAinto a gene product. In other embodiments, expression only includestranscription of the nucleic acid encoding genes of interest.

The nucleic acid encoding a gene product is under transcriptionalcontrol of a promoter. A “promoter” refers to a DNA sequence recognizedby the synthetic machinery of the cell, or introduced syntheticmachinery, required to initiate the specific transcription of a gene.The phrase “under transcriptional control” means that the promoter is inthe correct location and orientation in relation to the nucleic acid tocontrol RNA polymerase initiation and expression of the gene.

The term promoter will be used here to refer to a group oftranscriptional control modules that are clustered around the initiationsite for RNA polymerase II. Much of the thinking about how promoters areorganized derives from analyses of several viral promoters, includingthose for the HSV thymidine kinase (tk) and SV40 early transcriptionunits. These studies, augmented by more recent work, have shown thatpromoters are composed of discrete functional modules, each consistingof approximately 7-20 bp of DNA, and containing one or more recognitionsites for transcriptional activator or repressor proteins.

At least one module in each promoter functions to position the startsite for RNA synthesis. The best known example of this is the TATA box,but in some promoters lacking a TATA box, such as the promoter for themammalian terminal deoxynucleotidyl transferase gene and the promoterfor the SV40 late genes, a discrete element overlying the start siteitself helps to fix the place of initiation.

Additional promoter elements regulate the frequency of transcriptionalinitiation. Typically, these are located in the region 30-110 bpupstream of the start site, although a number of promoters have recentlybeen shown to contain functional elements downstream of the start siteas well. The spacing between promoter elements frequently is flexible,so that promoter function is preserved when elements are inverted ormoved relative to one another. In the tk promoter, the spacing betweenpromoter elements can be increased to 50 bp apart before activity beginsto decline. Depending on the promoter, it appears that individualelements can function either cooperatively or independently to activatetranscription.

The particular promoter employed to control the expression of a nucleicacid sequence of interest is not believed to be important, so long as itis capable of directing the expression of the nucleic acid in thetargeted cell. Thus, where a human cell is targeted, it is preferable toposition the nucleic acid coding region adjacent to and under thecontrol of a promoter that is capable of being expressed in a humancell. Generally speaking, such a promoter might include either a humanor viral promoter.

In various embodiments, the human cytomegalovirus (CMV) immediate earlygene promoter, the SV40 early promoter, the Rous sarcoma virus longterminal repeat, β-actin, rat insulin promoter andglyceraldehyde-3-phosphate dehydrogenase can be used to obtainhigh-level expression of the coding sequence of interest. The use ofother viral or mammalian cellular or bacterial phage promoters which arewell-known in the art to achieve expression of a coding sequence ofinterest is contemplated as well, provided that the levels of expressionare sufficient for a given purpose. By employing a promoter withwell-known properties, the level and pattern of expression of theprotein of interest following transfection or transformation can beoptimized.

Selection of a promoter that is regulated in response to specificphysiologic or synthetic signals can permit inducible expression of thegene product. For example in the case where expression of a transgene,or transgenes when a multicistronic vector is utilized, is toxic to thecells in which the vector is produced in, it may be desirable toprohibit or reduce expression of one or more of the transgenes. Examplesof transgenes that may be toxic to the producer cell line arepro-apoptotic and cytokine genes. Several inducible promoter systems areavailable for production of viral vectors where the transgene productmay be toxic.

The ecdysone system (Invitrogen, Carlsbad, Calif.) is one such system.This system is designed to allow regulated expression of a gene ofinterest in mammalian cells. It consists of a tightly regulatedexpression mechanism that allows virtually no basal level expression ofthe transgene, but over 200-fold inducibility. The system is based onthe heterodimeric ecdysone receptor of Drosophila, and when ecdysone oran analog such as muristerone A binds to the receptor, the receptoractivates a promoter to turn on expression of the downstream transgenehigh levels of mRNA transcripts are attained. In this system, bothmonomers of the heterodimeric receptor are constitutively expressed fromone vector, whereas the ecdysone-responsive promoter which drivesexpression of the gene of interest is on another plasmid. Engineering ofthis type of system into the gene transfer vector of interest wouldtherefore be useful. Cotransfection of plasmids containing the gene ofinterest and the receptor monomers in the producer cell line would thenallow for the production of the gene transfer vector without expressionof a potentially toxic transgene. At the appropriate time, expression ofthe transgene could be activated with ecdysone or muristeron A.

Another inducible system that would be useful is the Tet-Off™ or Tet-On™system (Clontech, Palo Alto, Calif.) originally developed by Gossen andBujard (Gossen and Bujard, 1992; Gossen et al., 1995). This system alsoallows high levels of gene expression to be regulated in response totetracycline or tetracycline derivatives such as doxycycline. In theTet-On™ system, gene expression is turned on in the presence ofdoxycycline, whereas in the Tet-Off™ system, gene expression is turnedon in the absence of doxycycline. These systems are based on tworegulatory elements derived from the tetracycline resistance operon ofE. coli. The tetracycline operator sequence to which the tetracyclinerepressor binds, and the tetracycline repressor protein. The gene ofinterest is cloned into a plasmid behind a promoter that hastetracycline-responsive elements present in it. A second plasmidcontains a regulatory element called the tetracycline-controlledtransactivator, which is composed, in the Tet-Off™ system, of the VP16domain from the herpes simplex virus and the wild-type tertracyclinerepressor. Thus in the absence of doxycycline, transcription isconstitutively on. In the Tet-On™ system, the tetracycline repressor isnot wild type and in the presence of doxycycline activatestranscription. For gene therapy vector production, the Tet-Off™ systemwould be preferable so that the producer cells could be grown in thepresence of tetracycline or doxycycline and prevent expression of apotentially toxic transgene, but when the vector is introduced to thepatient, the gene expression would be constitutively on.

In some circumstances, it may be desirable to regulate expression of atransgene in a gene therapy vector. For example, different viralpromoters with varying strengths of activity may be utilized dependingon the level of expression desired. In mammalian cells, the CMVimmediate early promoter if often used to provide strong transcriptionalactivation. Modified versions of the CMV promoter that are less potenthave also been used when reduced levels of expression of the transgeneare desired. When expression of a transgene in hematopoetic cells isdesired, retroviral promoters such as the LTRs from MLV or MMTV areoften used. Other viral promoters that may be used depending on thedesired effect include SV40, RSV LTR, HIV-1 and HIV-2 LTR, adenoviruspromoters such as from the E1A, E2A, or MLP region, AAV LTR, cauliflowermosaic virus, HSV-TK, and avian sarcoma virus.

Similarly tissue specific promoters may be used to effect transcriptionin specific tissues or cells so as to reduce potential toxicity orundesirable effects to non-targeted tissues. For example, promoters suchas the PSA, probasin, prostatic acid phosphatase or prostate-specificglandular kallikrein (hK2) may be used to target gene expression in theprostate. Similarly, the following promoters may be used to target geneexpression in other tissues (Table 5).

TABLE 5 Tissue specific promoters Tissue Promoter Pancreas insulinelastin amylase pdr-1 pdx-1 glucokinase Liver albumin PEPCK HBV enhanceralpha fetoprotein apolipoprotein C alpha-1 antitrypsin vitellogenin,NF-AB Transthyretin Skeletal muscle myosin H chain muscle creatinekinase dystrophin calpain p94 skeletal alpha-actin fast troponin 1 Skinkeratin K6 keratin K1 Lung CFTR human cytokeratin 18 (K18) pulmonarysurfactant proteins A, B and C CC-10 P1 Smooth muscle sm22 alphaSM-alpha-actin Endothelium endothelin-1 E-selectin von Willebrand factorTIE (Korhonen et al., 1995) KDR/flk-1 Melanocytes tyrosinase Adiposetissue lipoprotein lipase (Zechner et al., 1988) adipsin (Spiegelman etal., 1989) acetyl-CoA carboxylase (Pape and Kim, 1989) glycerophosphatedehydrogenase (Dani et al., 1989) adipocyte P2 (Hunt et al., 1986) Bloodβ-globin

In certain indications, it may be desirable to activate transcription atspecific times after administration of the gene therapy vector. This maybe done with such promoters as those that are hormone or cytokineregulatable. For example in gene therapy applications where theindication is a gonadal tissue where specific steroids are produced orrouted to, use of androgen or estrogen regulated promoters may beadvantageous. Such promoters that are hormone regulatable include MMTV,MT-1, ecdysone and RuBisco. Other hormone regulated promoters such asthose responsive to thyroid, pituitary and adrenal hormones are expectedto be useful in the present invention. Cytokine and inflammatory proteinresponsive promoters that could be used include K and T Kininogen(Kageyama et al., 1987), c-fos, TNF-alpha, C-reactive protein (Arcone etal., 1988), haptoglobin (Oliviero et al., 1987), serum amyloid A2, C/EBPalpha, IL-1, IL-6 (Poli and Cortese, 1989), Complement C3 (Wilson etal., 1990), IL-8, alpha-1 acid glycoprotein (Prowse and Baumann, 1988),alpha-1 antitypsin, lipoprotein lipase (Zechner et al., 1988),angiotensinogen (Ron et al., 1991), fibrinogen, c-jun (inducible byphorbol esters, TNF-alpha, UV radiation, retinoic acid, and hydrogenperoxide), collagenase (induced by phorbol esters and retinoic acid),metallothionein (heavy metal and glucocorticoid inducible), Stromelysin(inducible by phorbol ester, interleukin-1 and EGF), alpha-2macroglobulin and alpha-1 antichymotrypsin.

It is envisioned that cell cycle regulatable promoters may be useful inthe present invention. For example, in a bi-cistronic gene therapyvector, use of a strong CMV promoter to drive expression of a first genesuch as p16 that arrests cells in the G1 phase could be followed byexpression of a second gene such as p53 under the control of a promoterthat is active in the G1 phase of the cell cycle, thus providing a“second hit” that would push the cell into apoptosis. Other promoterssuch as those of various cyclins, PCNA, galectin-3, E2F1, p53 and BRCA1could be used.

Promoters that could be used according to the present invention includeLac-regulatable, chemotherapy inducible (e.g. MDR), and heat(hyperthermia) inducible promoters, Radiation-inducible (e.g., EGR (Jokiet al., 1995)), Alpha-inhibin, RNA pol III tRNA met and other amino acidpromoters, U1 snRNA (Bartlett et al., 1996), MC-1, PGK, -actin andalpha-globin. Many other promoters that may be useful are listed inWalther and Stein (1996).

It is envisioned that any of the above promoters alone or in combinationwith another may be useful according to the present invention dependingon the action desired. In addition, this list of promoters should not beconstrued to be exhaustive or limiting, those of skill in the art willknow of other promoters that may be used in conjunction with thepromoters and methods disclosed herein.

b. Enhancers

Enhancers are genetic elements that increase transcription from apromoter located at a distant position on the same molecule of DNA.Enhancers are organized much like promoters. That is, they are composedof many individual elements, each of which binds to one or moretranscriptional proteins. The basic distinction between enhancers andpromoters is operational. An enhancer region as a whole must be able tostimulate transcription at a distance; this need not be true of apromoter region or its component elements. On the other hand, a promotermust have one or more elements that direct initiation of RNA synthesisat a particular site and in a particular orientation, whereas enhancerslack these specificities. Promoters and enhancers are often overlappingand contiguous, often seeming to have a very similar modularorganization.

Below is a list of promoters additional to the tissue specific promoterslisted above, cellular promoters/enhancers and induciblepromoters/enhancers that could be used in combination with the nucleicacid encoding a gene of interest in an expression construct (Table 6 andTable 7). Additionally, any promoter/enhancer combination (as per theEukaryotic Promoter Data Base EPDB) could also be used to driveexpression of the gene. Eukaryotic cells can support cytoplasmictranscription from certain bacterial promoters if the appropriatebacterial polymerase is provided, either as part of the delivery complexor as an additional genetic expression construct.

In preferred embodiments of the invention, the expression constructcomprises a virus or engineered construct derived from a viral genome.The ability of certain viruses to enter cells via receptor-mediatedendocytosis and to integrate into host cell genome and express viralgenes stably and efficiently have made them attractive candidates forthe transfer of foreign genes into mammalian cells (Ridgeway, 1988;Nicolas and Rubenstein, 1988; Baichwal and Sugden, 1986; Temin, 1986).The first viruses used as gene vectors were DNA viruses including thepapovaviruses (simian virus 40, bovine papilloma virus, and polyoma)(Ridgeway, 1988; Baichwal and Sugden, 1986) and adenoviruses (Ridgeway,1988; Baichwal and Sugden, 1986). These have a relatively low capacityfor foreign DNA sequences and have a restricted host spectrum.Furthermore, their oncogenic potential and cytopathic effects inpermissive cells raise safety concerns. They can accommodate only up to8 kB of foreign genetic material but can be readily introduced in avariety of cell lines and laboratory animals (Nicolas and Rubenstein,1988; Temin, 1986).

c. Polyadenylation Signals

Where a cDNA insert is employed, one will typically desire to include apolyadenylation signal to effect proper polyadenylation of the genetranscript. The nature of the polyadenylation signal is not believed tobe crucial to the successful practice of the invention, and any suchsequence may be employed such as human or bovine growth hormone and SV40polyadenylation signals. Also contemplated as an element of theexpression cassette is a terminator. These elements can serve to enhancemessage levels and to minimize read through from the cassette into othersequences.

TABLE 6 ENHANCER Immunoglobulin Heavy Chain Immunoglobulin Light ChainT-Cell Receptor HLA DQ α and DQ β β-Interferon Interleukin-2Interleukin-2 Receptor MHC Class II 5 MHC Class II HLA-DRα β-ActinMuscle Creatine Kinase Prealbumin (Transthyretin) Elastase IMetallothionein Collagenase Albumin Gene α-Fetoprotein τ-Globin β-Globine-fos c-HA-ras Insulin Neural Cell Adhesion Molecule (NCAM)α1-Antitrypsin H2B (TH2B) Histone Mouse or Type I CollagenGlucose-Regulated Proteins (GRP94 and GRP78) Rat Growth Hormone HumanSerum Amyloid A (SAA) Troponin I (TN I) Platelet-Derived Growth FactorDuchenne Muscular Dystrophy SV40 Polyoma Retroviruses Papilloma VirusHepatitis B Virus Human Immunodeficiency Virus Cytomegalovirus GibbonApe Leukemia Virus

TABLE 7 Element Inducer MT II Phorbol Ester (TPA) Heavy metals MMTV(mouse mammary Glucocorticoids tumor virus) β-Interferon poly(rI)Xpoly(rc) Adenovirus 5 E2 Ela c-jun Phorbol Ester (TPA), H₂O₂ CollagenasePhorbol Ester (TPA) Stromelysin Phorbol Ester (TPA), IL-1 SV40 PhorbolEster (TPA) Murine MX Gene Interferon, Newcastle Disease Virus GRP78Gene A23187 α-2-Macroglobulin IL-6 Vimentin Serum MHC Class I Gene H-2kBInterferon HSP70 Ela, SV40 Large T Antigen Proliferin Phorbol Ester-TPATumor Necrosis Factor FMA Thyroid Stimulating Thyroid Hormone Hormone αGene Insulin E Box Glucose

7. Methods of Gene Transfer

In order to mediate the effect transgene expression in a cell, it willbe necessary to transfer the therapeutic expression constructs of thepresent invention into a cell. Such transfer may employ viral ornon-viral methods of gene transfer. This section provides a discussionof methods and compositions of gene transfer.

A. Viral Vector-Mediated Transfer

In certain embodiments, the NGVN gene is incorporated into a viralparticle to mediate gene transfer to a cell. Typically, the virus simplywill be exposed to the appropriate host cell under physiologicconditions, permitting uptake of the virus. The present methods may beadvantageously employed using a variety of viral vectors, as discussedbelow.

a. Adenovirus

Adenovirus is particularly suitable for use as a gene transfer vectorbecause of its mid-sized DNA genome, ease of manipulation, high titer,wide target-cell range, and high infectivity. The roughly 36 kB viralgenome is bounded by 100-200 base pair (bp) inverted terminal repeats(ITR), in which are contained cis-acting elements necessary for viralDNA replication and packaging. The early (E) and late (L) regions of thegenome that contain different transcription units are divided by theonset of viral DNA replication.

The E1 region (E1A and E1B) encodes proteins responsible for theregulation of transcription of the viral genome and a few cellulargenes. The expression of the E2 region (E2A and E2B) results in thesynthesis of the proteins for viral DNA replication. These proteins areinvolved in DNA replication, late gene expression, and host cell shutoff (Renan, 1990). The products of the late genes (L1, L2, L3, L4 andL5), including the majority of the viral capsid proteins, are expressedonly after significant processing of a single primary transcript issuedby the major late promoter (MLP). The MLP (located at 16.8 map units) isparticularly efficient during the late phase of infection, and all themRNAs issued from this promoter possess a 5′ tripartite leader (TL)sequence which makes them preferred mRNAs for translation.

In order for adenovirus to be optimized for gene therapy, it isnecessary to maximize the carrying capacity so that large segments ofDNA can be included. It also is very desirable to reduce the toxicityand immunologic reaction associated with certain adenoviral products.The two goals are, to an extent, coterminous in that elimination ofadenoviral genes serves both ends. By practice of the present invention,it is possible achieve both these goals while retaining the ability tomanipulate the therapeutic constructs with relative ease.

The large displacement of DNA is possible because the cis elementsrequired for viral DNA replication all are localized in the invertedterminal repeats (ITR) (100-200 bp) at either end of the linear viralgenome. Plasmids containing ITR's can replicate in the presence of anon-defective adenovirus (Hay et al., 1984). Therefore, inclusion ofthese elements in an adenoviral vector should permit replication.

In addition, the packaging signal for viral encapsidation is localizedbetween 194-385 bp (0.5-1.1 map units) at the left end of the viralgenome (Hearing et al., 1987). This signal mimics the proteinrecognition site in bacteriophage λ DNA where a specific sequence closeto the left end, but outside the cohesive end sequence, mediates thebinding to proteins that are required for insertion of the DNA into thehead structure. E1 substitution vectors of Ad have demonstrated that a450 bp (0-1.25 map units) fragment at the left end of the viral genomecould direct packaging in 293 cells (Levrero et al., 1991).

Previously, it has been shown that certain regions of the adenoviralgenome can be incorporated into the genome of mammalian cells and thegenes encoded thereby expressed. These cell lines are capable ofsupporting the replication of an adenoviral vector that is deficient inthe adenoviral function encoded by the cell line. There also have beenreports of complementation of replication deficient adenoviral vectorsby “helping” vectors, e.g., wild-type virus or conditionally defectivemutants.

Replication-deficient adenoviral vectors can be complemented, in trans,by helper virus. This observation alone does not permit isolation of thereplication-deficient vectors, however, since the presence of helpervirus, needed to provide replicative functions, would contaminate anypreparation. Thus, an additional element was needed that would addspecificity to the replication and/or packaging of thereplication-deficient vector. That element, as provided for in thepresent invention, derives from the packaging function of adenovirus.

It has been shown that a packaging signal for adenovirus exists in theleft end of the conventional adenovirus map (Tibbetts, 1977). Laterstudies showed that a mutant with a deletion in the E1A (194-358 bp)region of the genome grew poorly even in a cell line that complementedthe early (EIA) function (Hearing and Shenk, 1983). When a compensatingadenoviral DNA (0-353 bp) was recombined into the right end of themutant, the virus was packaged normally. Further mutational analysisidentified a short, repeated, position-dependent element in the left endof the Ad5 genome. One copy of the repeat was found to be sufficient forefficient packaging if present at either end of the genome, but not whenmoved towards the interior of the Ad5 DNA molecule (Hearing et al.,1987).

By using mutated versions of the packaging signal, it is possible tocreate helper viruses that are packaged with varying efficiencies.Typically, the mutations are point mutations or deletions. When helperviruses with low efficiency packaging are grown in helper cells, thevirus is packaged, albeit at reduced rates compared to wild-type virus,thereby permitting propagation of the helper. When these helper virusesare grown in cells along with virus that contains wild-type packagingsignals, however, the wild-type packaging signals are recognizedpreferentially over the mutated versions. Given a limiting amount ofpackaging factor, the virus containing the wild-type signals arepackaged selectively when compared to the helpers. If the preference isgreat enough, stocks approaching homogeneity should be achieved.

b. Retrovirus

The retroviruses are a group of single-stranded RNA virusescharacterized by an ability to convert their RNA to double-stranded DNAin infected cells by a process of reverse-transcription (Coffin, 1990).The resulting DNA then stably integrates into cellular chromosomes as aprovirus and directs synthesis of viral proteins. The integrationresults in the retention of the viral gene sequences in the recipientcell and its descendants. The retroviral genome contains threegenes—gag, pol and env—that code for capsid proteins, polymerase enzyme,and envelope components, respectively. A sequence found upstream fromthe gag gene, termed Ψ, functions as a signal for packaging of thegenome into virions. Two long terminal repeat (LTR) sequences arepresent at the 5′ and 3′ ends of the viral genome. These contain strongpromoter and enhancer sequences and also are required for integration inthe host cell genome (Coffin, 1990).

In order to construct a retroviral vector, a nucleic acid encoding apromoter is inserted into the viral genome in the place of certain viralsequences to produce a virus that is replication-defective. In order toproduce virions, a packaging cell line containing the gag, pol and envgenes but without the LTR and Ψ components is constructed (Mann et al.,1983). When a recombinant plasmid containing a human cDNA, together withthe retroviral LTR and Ψ sequences is introduced into this cell line (bycalcium phosphate precipitation for example), the Ψ sequence allows theRNA transcript of the recombinant plasmid to be packaged into viralparticles, which are then secreted into the culture media (Nicolas andRubenstein, 1988; Temin, 1986; Mann et al., 1983). The media containingthe recombinant retroviruses is collected, optionally concentrated, andused for gene transfer. Retroviral vectors are able to infect a broadvariety of cell types. However, integration and stable expression ofmany types of retroviruses require the division of host cells (Paskindet al., 1975).

An approach designed to allow specific targeting of retrovirus vectorsrecently was developed based on the chemical modification of aretrovirus by the chemical addition of galactose residues to the viralenvelope. This modification could permit the specific infection of cellssuch as hepatocytes via asialoglycoprotein receptors, should this bedesired.

A different approach to targeting of recombinant retroviruses wasdesigned in which biotinylated antibodies against a retroviral envelopeprotein and against a specific cell receptor were used. The antibodieswere coupled via the biotin components by using streptavidin (Roux etal., 1989). Using antibodies against major histocompatibility complexclass I and class II antigens, the infection of a variety of human cellsthat bore those surface antigens was demonstrated with an ecotropicvirus in vitro (Roux et al., 1989).

c. Adeno-Associated Virus

AAV utilizes a linear, single-stranded DNA of about 4700 base pairs.Inverted terminal repeats flank the genome. Two genes are present withinthe genome, giving rise to a number of distinct gene products. Thefirst, the cap gene, produces three different virion proteins (VP),designated VP-1, VP-2 and VP-3. The second, the rep gene, encodes fournon-structural proteins (NS). One or more of these rep gene products isresponsible for transactivating AAV transcription.

The three promoters in AAV are designated by their location, in mapunits, in the genome. These are, from left to right, p5, p19 and p40.Transcription gives rise to six transcripts, two initiated at each ofthree promoters, with one of each pair being spliced. The splice site,derived from map units 42-46, is the same for each transcript. The fournon-structural proteins apparently are derived from the longer of thetranscripts, and three virion proteins all arise from the smallesttranscript.

AAV is not associated with any pathologic state in humans.Interestingly, for efficient replication, AAV requires “helping”functions from viruses such as herpes simplex virus I and II,cytomegalovirus, pseudorabies virus and, of course, adenovirus. The bestcharacterized of the helpers is adenovirus, and many “early” functionsfor this virus have been shown to assist with AAV replication. Low levelexpression of AAV rep proteins is believed to hold AAV structuralexpression in check, and helper virus infection is thought to removethis block.

The terminal repeats of the AAV vector can be obtained by restrictionendonuclease digestion of AAV or a plasmid such as p201, which containsa modified AAV genome (Samulski et al., 1987), or by other methods knownto the skilled artisan, including but not limited to chemical orenzymatic synthesis of the terminal repeats based upon the publishedsequence of AAV. The ordinarily skilled artisan can determine, bywell-known methods such as deletion analysis, the minimum sequence orpart of the AAV ITRs which is required to allow function, i.e., stableand site-specific integration. The ordinarily skilled artisan also candetermine which minor modifications of the sequence can be toleratedwhile maintaining the ability of the terminal repeats to direct stable,site-specific integration.

AAV-based vectors have proven to be safe and effective vehicles for genedelivery in vitro, and these vectors are being developed and tested inpre-clinical and clinical stages for a wide range of applications inpotential gene therapy, both ex vivo and in vivo (Carter and Flotte,1996; Chatterjee et al., 1995; Ferrari et al., 1996; Fisher et al.,1996; Flotte et al., 1993; Goodman et al., 1994; Kaplitt et al., 1994;1996, Kessler et al., 1996; Koeberl et al, 1997; Mizukami et al., 1996).

AAV-mediated efficient gene transfer and expression in the lung has ledto clinical trials for the treatment of cystic fibrosis (Carter andFlotte, 1995; Flotte et al., 1993). Similarly, the prospects fortreatment of muscular dystrophy by AAV-mediated gene delivery of thedystrophin gene to skeletal muscle, of Parkinson's disease by tyrosinehydroxylase gene delivery to the brain, of hemophilia B by Factor IXgene delivery to the liver, and potentially of myocardial infarction byvascular endothelial growth factor gene to the heart, appear promisingsince AAV-mediated transgene expression in these organs has recentlybeen shown to be highly efficient (Fisher et al., 1996; Flotte et al.,1993; Kaplitt et al., 1994; 1996; Koeberl et al., 1997; McCown et al.,1996; Ping et al., 1996; Xiao et al., 1996).

d. Other Viral Vectors

Other viral vectors may be employed as expression constructs in thepresent invention. Vectors derived from viruses such as vaccinia virus(Ridgeway, 1988; Baichwal and Sugden, 1986; Coupar et al., 1988) canarypox virus, and herpes viruses may be employed. These viruses offerseveral features for use in gene transfer into various mammalian cells.

B. Non-Viral Transfer

Several non-viral methods for the transfer of expression constructs intocultured mammalian cells are contemplated by the present invention.These include calcium phosphate precipitation (Graham and Van Der Eb,1973; Chen and Okayama, 1987; Rippe et al., 1990) DEAE-dextran (Gopal,1985), electroporation (Tur-Kaspa et al., 1986; Potter et al., 1984),direct microinjection (Harland and Weintraub, 1985), DNA-loadedliposomes (Nicolau and Sene, 1982; Fraley et al., 1979), cell sonication(Fechheimer et al., 1987), gene bombardment using high velocitymicroprojectiles (Yang et al., 1990), and receptor-mediated transfection(Wu and Wu, 1987; Wu and Wu, 1988).

Once the construct has been delivered into the cell the nucleic acidencoding the therapeutic gene may be positioned and expressed atdifferent sites. In certain embodiments, the nucleic acid encoding thetherapeutic gene may be stably integrated into the genome of the cell.This integration may be in the cognate location and orientation viahomologous recombination (gene replacement) or it may be integrated in arandom, non-specific location (gene augmentation). In yet furtherembodiments, the nucleic acid may be stably maintained in the cell as aseparate, episomal segment of DNA. Such nucleic acid segments or“episomes” encode sequences sufficient to permit maintenance andreplication independent of or in synchronization with the host cellcycle. How the expression construct is delivered to a cell and where inthe cell the nucleic acid remains is dependent on the type of expressionconstruct employed.

In a particular embodiment of the invention, the expression constructmay be entrapped in a liposome. Liposomes are vesicular structurescharacterized by a phospholipid bilayer membrane and an inner aqueousmedium. Multilamellar liposomes have multiple lipid layers separated byaqueous medium. They form spontaneously when phospholipids are suspendedin an excess of aqueous solution. The lipid components undergoself-rearrangement before the formation of closed structures and entrapwater and dissolved solutes between the lipid bilayers (Ghosh andBachhawat, 1991). The addition of DNA to cationic liposomes causes atopological transition from liposomes to optically birefringentliquid-crystalline condensed globules (Radler et al., 1997). TheseDNA-lipid complexes are potential non-viral vectors for use in genetherapy.

Liposome-mediated nucleic acid delivery and expression of foreign DNA invitro has been very successful. Using the β-lactamase gene, Wong et al.,(1980) demonstrated the feasibility of liposome-mediated delivery andexpression of foreign DNA in cultured chick embryo, HeLa, and hepatomacells. Nicolau et al., (1987) accomplished successful liposome-mediatedgene transfer in rats after intravenous injection. Also included arevarious commercial approaches involving “lipofection” technology.

In certain embodiments of the invention, the liposome may be complexedwith a hemagglutinating virus (HVJ). This has been shown to facilitatefusion with the cell membrane and promote cell entry ofliposome-encapsulated DNA (Kaneda et al., 1989). In other embodiments,the liposome may be complexed or employed in conjunction with nuclearnonhistone chromosomal proteins (HMG-1) (Kato et al., 1991). In yetfurther embodiments, the liposome may be complexed or employed inconjunction with both HVJ and HMG-1. In that such expression constructshave been successfully employed in transfer and expression of nucleicacid in vitro and in vivo, then they are applicable for the presentinvention.

Other vector delivery systems which can be employed to deliver a nucleicacid encoding a therapeutic gene into cells are receptor-mediateddelivery vehicles. These take advantage of the selective uptake ofmacromolecules by receptor-mediated endocytosis in almost all eukaryoticcells. Because of the cell type-specific distribution of variousreceptors, the delivery can be highly specific (Wu and Wu, 1993).

Receptor-mediated gene targeting vehicles generally consist of twocomponents: a cell receptor-specific ligand and a DNA-binding agent.Several ligands have been used for receptor-mediated gene transfer. Themost extensively characterized ligands are asialoorosomucoid (ASOR) (Wuand Wu, 1987) and transferring (Wagner et al., 1990). Recently, asynthetic neoglycoprotein, which recognizes the same receptor as ASOR,has been used as a gene delivery vehicle (Ferkol et al., 1993; Peraleset al., 1994) and epidermal growth factor (EGF) has also been used todeliver genes to squamous carcinoma cells (Myers, EPO 0273085).

In other embodiments, the delivery vehicle may comprise a ligand and aliposome. For example, Nicolau et al., (1987) employedlactosyl-ceramide, a galactose-terminal asialganglioside, incorporatedinto liposomes and observed an increase in the uptake of the insulingene by hepatocytes. Thus, it is feasible that a nucleic acid encoding atherapeutic gene also may be specifically delivered into a cell typesuch as prostate, epithelial or tumor cells, by any number ofreceptor-ligand systems with or without liposomes. For example, thehuman prostate-specific antigen (Watt et al., 1986) may be used as thereceptor for mediated delivery of a nucleic acid in prostate tissue.

In another embodiment of the invention, the expression construct maysimply consist of naked recombinant DNA or plasmids. Transfer of theconstruct may be performed by any of the methods mentioned above whichphysically or chemically permeabilize the cell membrane. This isapplicable particularly for transfer in vitro, however, it may beapplied for in vivo use as well. Dubensky et al., (1984) successfullyinjected polyomavirus DNA in the form of CaPO₄ precipitates into liverand spleen of adult and newborn mice demonstrating active viralreplication and acute infection. Benvenisty and Neshif (1986) alsodemonstrated that direct intraperitoneal injection of CaPO₄ precipitatedplasmids results in expression of the transfected genes. It isenvisioned that DNA encoding a CAM also may be transferred in a similarmanner in vivo and express CAM.

Another embodiment of the invention for transferring a naked DNAexpression construct into cells may involve particle bombardment. Thismethod depends on the ability to accelerate DNA coated microprojectilesto a high velocity allowing them to pierce cell membranes and entercells without killing them (Klein et al., 1987). Several devices foraccelerating small particles have been developed. One such device relieson a high voltage discharge to generate an electrical current, which inturn provides the motive force (Yang et al., 1990). The microprojectilesused have consisted of biologically inert substances such as tungsten orgold beads.

8. Formulations and Routes for Administration to Patients

Where clinical applications are contemplated, it will be necessary toprepare pharmaceutical compositions—expression vectors, virus stocks,proteins, antibodies and drugs—in a form appropriate for the intendedapplication. Generally, this will entail preparing compositions that areessentially free of pyrogens, as well as other impurities that could beharmful to humans or animals.

One will generally desire to employ appropriate salts and buffers torender delivery vectors stable and allow for uptake by target cells.Buffers also will be employed when recombinant cells are introduced intoa patient. Aqueous compositions of the present invention comprise aneffective amount of the vector to cells, dissolved or dispersed in apharmaceutically acceptable carrier or aqueous medium. Such compositionsalso are referred to as inocula. The phrase “pharmaceutically orpharmacologically acceptable” refer to molecular entities andcompositions that do not produce adverse, allergic, or other untowardreactions when administered to an animal or a human. As used herein,“pharmaceutically acceptable carrier” includes any and all solvents,dispersion media, coatings, antibacterial and antifungal agents,isotonic and absorption delaying agents and the like. The use of suchmedia and agents for pharmaceutically active substances is well know inthe art. Except insofar as any conventional media or agent isincompatible with the vectors or cells of the present invention, its usein therapeutic compositions is contemplated. Supplementary activeingredients also can be incorporated into the compositions.

The active compositions of the present invention may include classicpharmaceutical preparations. Administration of these compositionsaccording to the present invention will be via any common route so longas the target tissue is available via that route. This includes oral,nasal, buccal, rectal, vaginal or topical. Alternatively, administrationmay be by orthotopic, intradermal, subcutaneous, intramuscular,intraperitoneal or intravenous injection. Such compositions wouldnormally be administered as pharmaceutically acceptable compositions,described supra.

The active compounds also may be administered parenterally orintraperitoneally. Solutions of the active compounds as free base orpharmacologically acceptable salts can be prepared in water suitablymixed with a surfactant, such as hydroxypropylcellulose. Dispersions canalso be prepared in glycerol, liquid polyethylene glycols, and mixturesthereof and in oils. Under ordinary conditions of storage and use, thesepreparations contain a preservative to prevent the growth ofmicroorganisms.

The pharmaceutical forms suitable for injectable use include sterileaqueous solutions or dispersions and sterile powders for theextemporaneous preparation of sterile injectable solutions ordispersions. In all cases the form must be sterile and must be fluid tothe extent that easy syringability exists. It must be stable under theconditions of manufacture and storage and must be preserved against thecontaminating action of microorganisms, such as bacteria and fungi. Thecarrier can be a solvent or dispersion medium containing, for example,water, ethanol, polyol (for example, glycerol, propylene glycol, andliquid polyethylene glycol, and the like), suitable mixtures thereof,and vegetable oils. The proper fluidity can be maintained, for example,by the use of a coating, such as lecithin, by the maintenance of therequired particle size in the case of dispersion and by the use ofsurfactants. The prevention of the action of microorganisms can bebrought about by various antibacterial an antifungal agents, forexample, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, andthe like. In many cases, it will be preferable to include isotonicagents, for example, sugars or sodium chloride. Prolonged absorption ofthe injectable compositions can be brought about by the use in thecompositions of agents delaying absorption, for example, aluminummonostearate and gelatin.

Sterile injectable solutions are prepared by incorporating the activecompounds in the required amount in the appropriate solvent with variousof the other ingredients enumerated above, as required, followed byfiltered sterilization. Generally, dispersions are prepared byincorporating the various sterilized active ingredients into a sterilevehicle which contains the basic dispersion medium and the requiredother ingredients from those enumerated above. In the case of sterilepowders for the preparation of sterile injectable solutions, thepreferred methods of preparation are vacuum-drying and freeze-dryingtechniques which yield a powder of the active ingredient plus anyadditional desired ingredient from a previously sterile-filteredsolution thereof.

As used herein, “pharmaceutically acceptable carrier” includes any andall solvents, dispersion media, coatings, antibacterial and antifungalagents, isotonic and absorption delaying agents and the like. The use ofsuch media and agents for pharmaceutical active substances is well knownin the art. Except insofar as any conventional media or agent isincompatible with the active ingredient, its use in the therapeuticcompositions is contemplated. Supplementary active ingredients can alsobe incorporated into the compositions.

For oral administration the polypeptides of the present invention may beincorporated with excipients and used in the form of non-ingestiblemouthwashes and dentifrices. A mouthwash may be prepared incorporatingthe active ingredient in the required amount in an appropriate solvent,such as a sodium borate solution (Dobell's Solution). Alternatively, theactive ingredient may be incorporated into an antiseptic wash containingsodium borate, glycerin and potassium bicarbonate. The active ingredientalso may be dispersed in dentifrices, including: gels, pastes, powdersand slurries. The active ingredient may be added in a therapeuticallyeffective amount to a paste dentifrice that may include water, binders,abrasives, flavoring agents, foaming agents, and humectants.

The compositions of the present invention may be formulated in a neutralor salt form. Pharmaceutically-acceptable salts include the acidaddition salts (formed with the free amino groups of the protein) andwhich are formed with inorganic acids such as, for example, hydrochloricor phosphoric acids, or such organic acids as acetic, oxalic, tartaric,mandelic, and the like. Salts formed with the free carboxyl groups canalso be derived from inorganic bases such as, for example, sodium,potassium, ammonium, calcium, or ferric hydroxides, and such organicbases as isopropylamine, trimethylamine, histidine, procaine and thelike.

Upon formulation, solutions will be administered in a manner compatiblewith the dosage formulation and in such amount as is therapeuticallyeffective. The formulations are easily administered in a variety ofdosage forms such as injectable solutions, drug release capsules and thelike. For parenteral administration in an aqueous solution, for example,the solution should lye suitably buffered if necessary and the liquiddiluent first rendered isotonic with sufficient saline or glucose. Theseparticular aqueous solutions are especially suitable for intravenous,intramuscular, subcutaneous and intraperitoneal administration. In thisconnection, sterile aqueous media which can be employed will be known tothose of skill in the art in light of the present disclosure. Forexample, one dosage could be dissolved in 1 ml of isotonic NaCl solutionand either added to 1000 ml of hypodermoclysis fluid or injected at theproposed site of infusion, (see for example, “Remington's PharmaceuticalSciences” 15th Edition, pages 1035-1038 and 1570-1580). Some variationin dosage will necessarily occur depending on the condition of thesubject being treated. The person responsible for administration will,in any event, determine the appropriate dose for the individual subject.Moreover, for human administration, preparations should meet sterility,pyrogenicity, general safety and purity standards as required by FDAOffice of Biologics standards.

9. Examples

The following examples are included to demonstrate preferred embodimentsof the invention. It should be appreciated by those of skill in the artthat the techniques disclosed in the examples which follow representtechniques discovered by the inventor to function well in the practiceof the invention, and thus can be considered to constitute preferredmodes for its practice. However, those of skill in the art should, inlight of the present disclosure, appreciate that many changes can bemade in the specific embodiments which are disclosed and still obtain alike or similar result without departing from the spirit and scope ofthe invention.

Example 1 Materials and Methods

Patients and Families

Patients were identified through the Department of Opthalmology at theUniversity of Iowa or by collaborating investigators at otherinstitutions. Signed, informed consent was obtained from each patientprior to the collection of a sample of whole blood (5 to 10 ml) usingprotocols approved by the Institutional Review Board at the Universityof Iowa.

DNA Isolation

Genomic DNA was isolated from whole blood according to methods that havebeen published previously. YAC DNA was isolated using the DNA-Pure yeastgenomic kit (CPG, Inc.). BAC DNA was prepared via an alkaline lysisprotocol as implemented in the Wizard Plus Miniprep Kit (Promega) withthe following modification to the protocol. Instead of loading thesupernatant onto a vacuum column, it was precipitated with a 2× volumeof absolute EtOH. In addition, 150 μl volumes were used for thecommercial solutions in place of the 200 μl volumes suggested in theprotocol. The precipitated DNA was then washed with 70% EtOH and dried.The DNA pellet was then resuspended in 50 μl of ddH₂O. Finally, plasmidDNA was prepared using a Wizard Plus Miniprep kit (Promega) followingthe recommended protocol. Culture sizes for DNA preparation from YACs,BACs and plasmids were 1.5 ml of the appropriate media and antibioticsfor each construct.

Marker Typing

PCR amplification for the analysis of short tandem repeat polymorphisms(STRPs) was performed using 20 ng of genomic DNA in 5 μl reactionscontaining 0.5 μl of 10×PCR buffer [100 mM Tris-HCl (pH 8.8), 500 mMKCl, 15 mM MgCl₂, 0.01% gelatin (w/v)], 200 μM each of dATP, dCTP, dGTPand dTTP, 2.5 μmol of each primer and 0.2 units of Taq polymerase (BMB,ISC). Samples were subjected to 35 cycles of 94° C. for 30 sec, (50, 52,55 or 57° C. as required) for 30 sec and 72° C. for 30 sec.Amplification products were electrophoresed on 6% polyacrylamide gelscontaining 7.7 M urea at 60 W for approximately 2 h. The bands weredetected by silver staining. Bassam (1991).

Marker typing for physical mapping was performed on 2% agarose gelsusing a PCR reaction size of 10 μl. Reaction conditions were asdescribed above with the following exceptions. For markers that proveddifficult to amplify using the standard Taq polymerase, the inventorssubstituted an equal amount of AmpliTaq (ABI) along with an initialincubation of the PCR mixture at 94° C. for 10 minutes. For PCRreactions involving YAC, BAC or plasmid DNA, 1 to 2 ng of DNA wasutilized as template. For colony PCR, a small number of cells wereinoculated into 20 μl of ddH₂O. One μl of this suspension was used astemplate for the PCR reaction.

Oligonucleotide primers for the STRPs were obtained as MapPairs(Research Genetics or Integrated DNA Technologies). The custom primersrequired for this study were designed using the PRIMER 0.5 program andsynthesized commercially (Research Genetics). Size standards for the 2%agarose gels were 100 bp ladder (Gibco/BRL) and for the denaturingacrylamide gels a 50 bp ladder (Gibco/BRL). For the 0.8% agarose gels,lambda DNA digested with Styl was used as a size marker.

YAC, BAC and cDNA Identification

Initially, YACs were identified by searching a database at the WhiteheadInstitute/MIT Genome Center (http://www-genome.wi.mit.edu) (Hudson etal., 1995) with STSs known to be in the 16q21 region. Subsequently, YACsand BACs were identified by a PCR-based screening assay of pooledlibraries (Research Genetics) using various STSs within each region.ESTs were identified by a BLASTN search of the public dbEST databaseavailable through a web interface NCBI. Altschul & Lipman (1990).

Gene Identification and Characterization

Raw SCF files from ABI 373A and 377 sequencers were imported directlyinto the Sequencher v3.1 program (GeneCodes). Contigs were generated bycomparing all fragments in a project with the parameters of at least a50 bp overlap in sequence with a 80% level of homology. Genomic sequenceof BACs from the 16q21 region was submitted to the BLAST server at NCBIfor a BLASTN analysis on both the NR and dbEST databases. Altschul &Lipman (1990). Any region which gave a significant score (p<10⁻⁵) wasalso submitted for a BLASTX screen of the SWISS-PROT database. ESTsequence was obtained from GENBANK and SCF files from the WashU-Merckftp site (ftp://genome.wustl.edu).

Sequencing Plasmids and PCR Products

PCR products for sequencing were amplified in a 50 μl reaction size andpurified using the Quiaquick PCR Clean-up kit (Promega). 500 ng ofplasmid DNA (in 4.5 μl) or 4.5 μl of purified PCR product was used astemplate for a sequencing reaction. One μl of primer (20 pmoles) and 4.5μl of terminator sequencing mix (Amersham) was added for a finalreaction size of 10 μl. Cycling conditions were performed as specifiedby the manufacturer. The sequencing reactions were precipitated in thepresence of linear acrylamide and resuspended in 2 μl of loading buffer.The reactions were analyzed on an ABI 377 using a run time of 3 h.

Mutation Detection and Confirmation

Mutation detection was performed using single strand conformationpolymorphism (SSCP) analysis and direct sequencing of PCR products. PCRproducts were electrophoresed on SSCP gels (5 ml glycerol, 5 ml 5×TBE,12.5 ml 37.5:1 acrylamide/bis and 77.5 ml ddH₂O) for 3 to 4 hr in0.25×TBE at room temperature. Gels were silver stained as describedabove. Abnormal variants were sequenced and compared to a control sampleto detect any changes from that of the normal sequence. Mutations wereconfirmed by amplification-refractory mutation system (ARMS) analysis.Newton (1989).

Northern Blot Analysis

Human Multiple Tissue Northern (MTN) blots I and III and Human Fetal MTNBlot II were obtained from Clontech (San Francisco, Calif.). The blotswere hybridized with a 300 bp DNA probe derived from the 3′ UIR of thehuman NGVN gene. The probe was amplified by PCR using the NGVN-forward(5′-AATAACCTTGGTGAGTTGTAC-3′) and NGVN-reverse(5′-ATACAAATGGGCAATTCTGAT-3′) primers. The probe was labeled with³²P-dCTP using Ready-To-Go DNA Labeling Beads (Amersham PharmaciaBiotech, Piscataway, N.J.). Hybridization and autoradiography wereperformed as described previously. The blots were stripped ofradioactivity and re-hybridized with a cDNA probe for β-actin (Clontech,San Francisco, Calif.) to assess equal loading of the RNA.

Example 2 Results

Clinical Data

The clinical features of the large Bedouin kindred (pedigree 1) havepreviously been described. Briefly, all of the cardinal features of BBSwere present in at least some of the members of this family. None of thepatients had spastic paraplegia, colobomas or deafness, diagnosticfeatures of Laurence-Moon, Biemond and Alstrom syndromes, respectively.Pedigree 2 consisted of four affected individuals of Kurdish ancestry,all of which had at least three of the cardinal features of BBSsyndrome. Within the two families there was a clear dichotomy betweenaffected and unaffected individuals in that none of the unaffectedindividuals had any of the features of Bardet-Biedl syndrome.

Affected individual from both families had very similar distributions ofpolydactyly, usually affecting both upper and lower extremities. All butone patient had polydactyly affecting at least three limbs, and theexception had two limb polydactyly. Obesity was more apparent in kindred2 compared to kindred 1. Hypogenitalism was apparent in male members ofboth families. Two patients in family 1 had unilateral renal hypoplasia.Retinal degeneration was a striking feature of the disorder in bothfamilies. All affected probands used in this study had at least three ofthe cardinal features of BBS. The minimal criteria for inclusion in thestudy were the diagnostic features of obesity, polydactyl), andpigmented retinopathy.

Definition of Critical Interval by Genetic Analysis

In 1993, linkage studies and haplotype analysis of a large inbredBedouin kindred mapped the BBS2 locus to an 18 cM region within 16q21flanked by the markers D16S419 and D16S265. Analysis of additionalgenetic markers within this region allowed the critical interval to benarrowed to approximately 6 cM. This proved to be the best estimate ofthe critical interval that was possible based upon the geneticinformation provided by the affected individuals in this family. As BBSis a highly penetrant disorder, it was decided that the study ofunaffected individuals within the pedigree might allow for the furtherrefinement of the critical interval with a high level of confidence inthe results.

One of the unaffected individuals from the Bedouin pedigree was found tohave a recombination event at the distal end of the critical intervalthat narrowed the distal flank to a region within the BACRP_(—)11-152E5. However, no additional refinement was possible for theproximal flanking region using information from unaffected individualsfrom the pedigree. Over 40 additional DNA samples were obtained fromunaffected members of the Bedouin tribe that was segregating the BBS2locus in an attempt to further refine the critical interval. Given thehigh penetrance of BBS, the detection of a region containinghomozygosity for the affected haplotype in an unaffected individualwould strongly suggest that the BBS2 gene would be excluded from theregion. Analysis of these additional samples yielded an unaffectedindividual who had inherited the affected haplotype in the homozygousstate at the proximal end of the critical region. This allowed theinventors to exclude the BBS2 gene from a region that was proximal toD16S408. The refined critical interval included an approximately 2 cMregion between the markers D16S408 and 152e5-CA.

Physical Mapping

To facilitate the cloning and characterization of the BBS2 gene, theinventors constructed a physical map of the critical interval. Aninitial physical map that was based on YAC clones allowed for lowresolution localization of genetic markers and candidate genes withinthe critical interval. Once the genetic interval was refined to thesmallest size possible, the physical map was converted to one that wasbased on BAC clones. The smaller size of the BAC clones allowed forhigher resolution mapping of genetic markers and candidate genes withinthe interval. Radiation hybrid mapping using the Stanford G3 mappingpanel was used to confirm the order obtained from the BAC-based physicalmaps as well as to anchor this region within the Stanford chromosome 16G3 radiation hybrid map.

Candidate Gene Identification

The BAC-based physical map was used to select a subset of BACs forsample sequencing at 1× coverage. The sequence information obtained fromsample sequencing was combined with that available from the publicsequence databases and used for the identification of candidate genesfor BBS2. BLASTN analysis was performed against the nr and dbESTdatabases that are maintained by NCBI. This allowed the inventors toidentify a number of unique genes and Unigene EST clusters. Over 30unique genes or EST clusters were identified, not including the multiplemetallothionein genes that are known to map within the region. The geneswere prioritized for mutation screening based on criteria including (i)availability of known cDNA and/or genomic sequence, (ii) knownexpression pattern of the gene consistent with the BBS phenotype and(iii) the availability of any functional information. Although the useof information from unaffected individuals to narrow the criticalinterval was postulated to be reliable, an attractive candidate genethat mapped within the more conservative interval defined by an“affected-only” analysis was not strictly ruled out, but deemed to be oflower priority for analysis.

Mutation Screening of Candidate Genes

A second inbred pedigree consisting of 4 affected individuals was alsofound to be linked to the BBS2 locus. Genotyping of DNA from the threeaffected individuals from whom DNA was available for demonstrated thatall were homozygous for the same haplotype. This haplotype was not foundin the homozygous state in any of the unaffected individuals in thefamily. The affected haplotype was found to be different than thatsegregating within the large inbred Bedouin family suggesting that themutation in each family would likely be different.

The availability of two inbred BBS2 pedigrees with likely independentmutations allowed the inventors to conduct a sequencing-based mutationscreen of BBS2 candidate genes. PCR amplicons that covered the codingsequence and consensus splice sites for each candidate gene wereamplified from genomic DNA from an affected individual from each of thetwo BBS2 pedigrees, and the amplification products were directlysequenced. The DNA sequence generated from the two samples were comparedwith each other as well as to sequence available in the public DNAsequence databases. Fifteen candidate genes were screened withoutfinding any evidence for pathological variants.

NGVN Gene Structure and Expression Profile

UniGene EST cluster Hs.24809 was selected for analysis based on thesuggestion a of a broad expression pattern and on map position withinthe narrowest candidate interval. The UniGene cluster contained 194 ESTsas well as 6 mRNA sequences. When these sequences were assembled intocontigs, two distinct, unique contigs were created. Both contigs werefound to map to the same BAC (RP_(—)11-5A3) that was located within theBBS2 critical interval on chromosome 16.

One of the contigs was found to contain an open reading frame of 1461bp. Partial gene structure could be determined for this genes whichyielded 9 exons for analysis. The second contig was found to contain anopen reading frame of 2,163 bp. The complete gene structure wasascertained for this gene, now referred to as negevin (NGVN). Comparisonof cDNA sequence with genomic sequence revealed a total of 17 exons.Both genes were screened for mutations. While the mutation screen of thefirst gene produced no evidence of pathologically significant variants,a number of mutations were detected in the NGVN gene.

NGVN was amplified from a human fetal cDNA library and sequenced toconfirm the cDNA sequence that was predicted from the EST contig.Sixty-six of the 193 ESTs from UniGene cluster Hs.24809 were assigned tothe NGVN contig. The tissue distribution of these ESTs suggested thatNGVN was a widely expressed gene. Northern blot analysis confirmed thebroad expression pattern of NGVN and revealed a NGVN mRNA size estimateof approximately 3.0 kb. This size estimate agrees well with the sizepredicted from the genomic DNA sequence. A minor Northern blot band ofsmaller molecular weight was apparent in trachea tissue, suggestingalternative splicing.

NGVN Mutations

Mutation screening of NGVN produced strong mutation candidates in bothof the linked BBS2 families that were part of the initial mutationscreen. The smaller BBS2-linked family was found to harbor a 1 bpdeletion in exon 8 (940delA). The mutation was found in the homozygousstate in all three of the affected individuals, and was not found in thehomozygous state in unaffected family members. The frameshift has notbeen detected to date in any other family or proband that has beenexamined, or in 96 control individuals.

Two sequence variants were detected in the large, inbred Bedouin BBSfamily. An A to G transition at nucleotide position 367 (Ile123Val) wasdetected in exon 3. Ile123Val is conservative and thus was not judged tobe responsible for the BBS phenotype in the family. A second variant, aT to G transversion, was found at nucleotide position 224 (Val75Gly) inexon 2 that produced a non-conservative amino acid change. This variantis postulated to be the disease causing mutation in this family. BothDNA sequence variants segregate with the BBS phenotype within the familyin that all affected individuals were homozygous for the sequencevariant, all obligate carriers (parents of BBS patients) wereheterozygous for the variant, and no unaffected individuals werehomozygous for the variant.

The detection of mutations in the two BBS2 families prompted theinventors to sequence the NGVN gene from a panel of 18 unrelated BBSprobands in an attempt to identify additional mutations in NGVN. A 1 bpinsertion (1206insA) was observed in exon 10 in the homozygous state ina single proband (BB31-1). The insertion results in a frameshift thatpredicts premature termination of translation five amino acidsdownstream from the insertion. One proband harbored an exon 8 nonsensemutations at codon 275 (Arg275Stp) in the homozygous state. A secondexon 8 nonsense mutation (Arg272Stp) was found in the heterozygous statein another proband. In all, mutations were observed in 3 of 18 unrelatedBBS probands.

In addition to the mutations described above, other sequence variantswere found that are likely to be benign sequence variations. Theconservative Ile123Val change was found in the heterozygous state in twoof the probands (BBI-1 and BB55-1) as well as in control individuals.Furthermore, an A1413C transversion resulting in a synonymous codonchange was observed in one proband (BB55-1).

Evolutionary Conservation

Homology screening of NGVN against the public sequence databasesdemonstrates that NGVN has strong sequence homology to genes from anumber of other organisms. Sequence for the mouse orthologue for NGVNwas obtained by PCR from a 17 day fetal mouse cDNA library to supplementthe sequence that was available from GenBank. The mouse gene is 90%identical and 95% similar to the human gene within the coding region atthe protein level. Sequence for the rat and zebrafish orthologues ofNGVN were obtained using the same methodology as was employed toascertain the sequence for the mouse orthologue. The rat orthologue wasfound to be 89% identical and 94% similar at the protein level. Thezebrafish orthologue was found to be 74% identical and 84% similar. Areduced level of homology was found for organisms such as C. elegans,Chlamydomonas and Trypanosoma (30 to 46% identical; 49 to 57% similar).

In order to further investigate the disease causing nature of the exon 2Val75Gly variant, sequence was obtained from a number of organisms todetermine the level of sequence conservation within this region. Valinewas found at this position in human, bovine, rabbit, rat, mouse andzebrafish. In C. elegans, Trypanosoma and Chlamydomonas, theconservative substitution of isoleucine was found at this position.There is a high level of conservation at a number of locations withinthis region as well as within the region surrounding the Ile75Valvariant in exon 3. However, the isoleucine at codon 123 shows a lowerlevel of conservation, consistent with its postulated assignment as alikely benign sequence variant.

Lack of Homology to MKKS and Other Known Genes

As the BBS6 gene, MKKS, has been provisionally identified as achaperonin, the inventors attempted to identify homology between NGVNand known chaperonin or chaperonin-like genes. No homology was found toany genes with known function by both BLAST analysis or by searching forfunctional domains within NGVN.

All of the composition and methods disclosed and claimed herein can bemade and executed without undue experimentation in light of the presentdisclosure. While the compositions and methods of this invention havebeen described in terms of preferred embodiments, it will be apparent tothose of skill in the art that variations may be applied to thecompositions and methods and in the steps or in the sequence of steps ofthe method described herein without departing from the concept, spiritand scope of the invention. More specifically, it will be apparent thatcertain agents which are both chemically and physiologically related maybe substituted for the agents described herein while the same or similarresults would be achieved. All such similar substitutes andmodifications apparent to those skilled in the art are deemed to bewithin the spirit, scope and concept of the invention as defined by theappended claims.

REFERENCES

The following references, to the extent that they provide exemplaryprocedural or other details supplementary to those set forth herein, arespecifically incorporated herein by reference:

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What is claimed is:
 1. An isolated and purified nucleic acid encoding ahuman negevin (NGVN) polypeptide, wherein the polypeptide comprises SEQID NO: 2 or a variant thereof comprising one or more of the followingchanges: Va175Gly, Arg272Stp, Ile123Val, or a frameshift starting atresidue 314 or residue 403 of SEQ ID NO:2 and which hybridize to anucleic acid encoding SEQ ID NO:2 under high stringency conditions. 2.The nucleic acid of claim 1, wherein said polypeptide comprises thesequence of SEQ ID NO:2 wherein said nucleic acid comprises the sequenceof SEQ ID NO:1 or SEQ ID NO:
 3. 3. The nucleic acid of claim 1, whereinthe nucleic acid comprises the sequence of SEQ ID NO:1 or SEQ ID NO:3 orone or more of the changes selected from the group consisting of T₂₂₄→G,C₈₁₄→T, C₈₂₃→T, A₃₆₇→G, A₁₄₁₃→C, A₉₄₀del and 1206insA of SEQ ID NO:1. 4.The nucleic acid of claim 1, wherein the nucleic acid comprises thesequence of SEQ ID NO:3 except for one or one or more of the changesselected from the group consisting of T₂₂₄→G, C₈₁₄→T, C₈₂₃→T, A₃₈₇→G,A₁₄₁₃→C, A₉₄₀del and 1206insA.
 5. The nucleic acid of claim 1, furthercomprising a promoter.
 6. The nucleic acid of claim 5, wherein saidpromoter is selected from the group consisting of an inducible promoter,a constitutive promoter, and a tissue specific promoter.
 7. The nucleicacid of claim 5, wherein said promoter is active in eukaryotic cells. 8.The nucleic acid of claim 5, further comprising a selectable marker. 9.The nucleic acid of claim 5, further comprising a poly-adenylationsignal.
 10. The nucleic acid of claim 5, further comprising an origin ofreplication.
 11. The nucleic acid of claim 10, wherein said nucleic acidis part of a replicable vector.
 12. The nucleic acid of claim 11,wherein said vector is a viral vector.
 13. The nucleic acid of claim 12,wherein said viral vector is selected from the group consisting of aretroviral vector, an adenoviral vector, an adeno-associated viralvector, a herpes viral vector, a polyoma viral vector, a vaccinia viralvector and a lentiviral vector.
 14. The nucleic acid of claim 12,wherein said viral vector is located within a viral particle.
 15. Thenucleic acid of claim 10, wherein said vector is a non-viral vector.